This information will help you follow a low-microbial diet. Eating a low-microbial diet will reduce your risk of getting sick while your immune system is weak, such as after chemotherapy, radiation therapy, or a bone marrow or stem cell transplant.

The first section of this resource has information on how to keep your food safe. The second section explains what foods and beverages are safe to eat and drink while on a low-microbial diet. Do not make any changes to this diet until you have talked to someone on your healthcare team. This includes your doctor, nurse, nurse practitioner, or dietitian.

Allogeneic and autologous stem cell transplant patients should follow the diet for the first 100 days post transplant. Please speak to your healthcare team about whether you need to continue to follow the diet after the 100-day period is over.

Food Safety Guidelines

What are microbes?

Microbes are tiny living organisms, such as bacteria, viruses, yeast, and molds. They can get into food by infecting the animal the food comes from. Microbes can also get into food when it is being processed or prepared. When microbes get into foods, they can cause infections, especially if you have a low white blood cell count (neutropenia).

Microbes can attach to foods and grow, but you can’t always see, smell, or taste them. They are more likely to grow on:
  • Milk and other dairy food items that are not refrigerated.
  • Unpasteurized cheeses (e.g., Brie or feta).
  • Undercooked and raw eggs and foods that have raw eggs (e.g., cookie dough and Caesar salad dressing).
  • Undercooked or raw meat, poultry (chicken and turkey), and seafood including smoked seafood (e.g. smoked salmon or trout).
  • Certain fruits and vegetables (see the Fruits and Vegetable list in the “What to Eat on a Low-Microbial Diet” section).
  • Unpasteurized or untreated juices (e.g., fresh-squeezed juices).
  • Vegetable sprouts (e.g., raw alfalfa, soy bean, and radish sprouts).

Buying foods that are safe to eat

  • Don’t buy canned foods if the can has dents or is swollen.
  • Don’t buy food in jars if the jar is cracked or the lid is not tightly closed.
  • Only buy eggs that are refrigerated in the store. Check the eggs by opening the carton to see if any are broken or cracked.
  • Separate ready-to-eat and raw foods. Put raw meat, poultry, seafood, and other raw foods in plastic bags before they go into your shopping cart.
  • Pick up your milk and other cold foods at the end of your shopping trip. This decreases the time these items will spend outside of the refrigerator.
  • Check containers for the expiration date. Buy and use food before that date.

Transporting food safely

  • After grocery shopping, go directly home, so that you can put your perishable food (food that can go bad quickly) into the refrigerator or freezer right away.
  • Never leave perishable foods in a hot car.
    • If you need to make a stop after grocery shopping or your trip from the grocery store to your home is long, place the perishable foods in an insulated bag or cooler with ice or frozen gel packs. These will keep the food cold until you can store it safely at home.

Storing food safely

  • Store food immediately after shopping.
  • Put eggs and milk inside the refrigerator; don’t store them in the door. The temperature inside the refrigerator will stay cooler than in the door area.

Keeping your kitchen clean

  • Keep an area of your kitchen clean for preparing and eating food. This will help prevent the spread of microbes.
  • Use paper towels or clean cloths instead of sponges to clean kitchen surfaces.
  • Use an antibacterial cleaning spray to clean surfaces. Look for products that have bleach or ammonia. Examples are Lysol® Food Surface Sanitizer and Clorox® Clean-Up® Cleaner.

Using cutting boards and equipment

  • Use cutting boards that are made out of thick plastic, marble, glass, or ceramic. These materials are nonporous, meaning that food or liquid substances can’t absorb into them. Don’t use wood or other porous surfaces that can absorb food and liquids.
  • Wash cutting boards and knives with hot soapy water before using them to cut the next food. As an extra precaution, wash your cutting boards with a kitchen sanitizer. Throw out worn or hard-to-clean cutting boards.

Handling food safely

  • Wash your hands thoroughly:
    • Before preparing or eating food
    • After preparing raw poultry, meat, fish, or seafood
    • After handling garbage
  • Thoroughly rinse fresh fruits and vegetables under running tap water. Rinse skins and rinds before cutting or peeling. Never use bleach or detergent to wash fresh fruits and vegetables.
  • Rub firm-skinned fruits and vegetables under running warm tap water or scrub them with a clean vegetable brush while rinsing with running tap water.
  • Remove and throw away any damaged or bruised areas on fruits or vegetables.
  • Cook all foods thoroughly.
  • Separate raw meats from ready-to-eat foods.
  • Thaw foods by using one of the following methods:
    • Put the food item in the refrigerator 1 day before cooking.
    • Use the defrost setting on a microwave. Cook right away.
  • Keep your refrigerator at a temperature of 33° F to 40° F (0.6°C to 4.4°C).
  • Keep your freezer at a temperature of 0° F (-17.8°C) or below.
  • Use a food thermometer to check the internal temperatures of cooked and reheated foods.
  • Don’t eat hamburgers and other meat products if the meat looks undercooked. Cook the meat until it is grey and the juices run clear.
  • Cook fish until it flakes.
  • Cook egg whites and yolks until they are firm.
  • Cook all meats to the minimum internal temperatures listed in the chart below.
Safe Minimum Internal Temperatures
Egg and Egg Dishes
Cook until yolk and white are firm
Egg dishes
160° F
Egg sauces
160° F
Ground Meat and Meat Mixtures
Turkey and chicken
165° F
Beef, hamburgers, veal, lamb, and pork
160° F
Fresh Beef, Veal, and Lamb
Well done
170° F
Fresh Pork
Well done
170° F
160° F
Precooked, cured ham
140° F
All products
165° F
All (raw/fresh)
145° F

Eating leftovers

  • Refrigerate leftovers in shallow containers immediately after eating.
  • Reheat the following leftovers to an internal temperature of at least 165°F for at least 15 seconds:
    • Poultry
    • Stuffed meat, poultry, or fish
    • Ground meat
    • Pork, beef, veal, and lamb
    • Hard-boiled eggs
  • When reheating leftovers in the microwave, stir, cover, and rotate the food so that it heats evenly. Heat the food until it reaches 165° F throughout, as measured with a food thermometer.
  • Sauces, soups, and gravies should be reheated by bringing them to a boil.
  • Be sure to let the food cool so you don’t burn your mouth.
  • Eat reheated leftovers within 1 hour of reheating.
  • Don’t eat leftovers more than 2 days old.
  • Don’t eat any food that has already been reheated once.
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What to Eat on a Low-Microbial Diet

Food Group
What to Eat
What to Avoid
Breads, Grains,
and Cereals
  • All breads, rolls, bagels, English muffins, waffles, French toast, muffins, pancakes, and sweet rolls
  • Potato chips, corn chips, tortilla chips, popcorn, and pretzels
  • Any cooked or ready-to-eat cereal purchased prepackaged from a store
  • Rice, pasta, and other cooked grains
  • Foods with raw (not cooked or baked) grains (e.g., uncooked corn or raw oats)
  • Undercooked or raw brewer’s yeast
Dairy Products
  • Grade A commercially available milk and milk products
  • Yogurts, including those made with live cultures (e.g., Dannon®)
  • Sour cream
  • Puddings made at home or bought prepackaged from a store
  • Prepackaged ice cream, frozen yogurt, sherbet, popsicles, ice cream bars, and fresh homemade milkshakes
  • Eggnog
  • Commercially sterile, ready-to-feed, and liquid concentrate infant formulas
  • Dry, refrigerated, or frozen pasteurized whipped topping
Pasteurized Cheese
  • Processed cheese slices and spreads, cream cheese, cottage cheese, and ricotta cheese
  • Commercially packaged hard and semi-soft cheese such as American, mild cheddar, pasteurized mozzarella, Monterey jack, Swiss, and shelf-stable (foods that can be safely stored at room temperature) grated Parmesan (e.g., Kraft®)
  • Cooked soft cheeses, such as Brie, Camembert, feta, and farmer’s cheese.
  • Dairy products, such as raw milk
  • Eggnog (homemade)
  • Yogurt (usually homemade)
  • Soft serve ice cream or yogurt
  • Unrefrigerated, cream-filled pastry products
  • Fermented dairy products
  • Products with probiotics added after pasteurization
  • All cheese made from unpasteurized milk including soft cheeses, such as Brie, farmer’s cheese, Camembert, Mexican-style cheese (queso blanco and queso fresco), and goat cheese, and unpasteurized mozzarella cheese.
  • All mold-ripened cheeses and soft cheeses, such as Roquefort, Muenster, Stilton, havarti, Edam, Gorgonzola, blue cheese, sharp cheddar, and feta
  • Cheeses from delis
  • Cheeses that contain chili peppers or other uncooked vegetables
  • Well-cooked eggs (firm white and yolk)
  • Pasteurized eggs, pasteurized egg substitutes (such as Egg Beaters®), and powdered egg whites
  • Undercooked or raw eggs and unpasteurized egg substitutes
  • Salad dressings containing raw eggs (e.g., Caesar salad dressing)
Meat, Meat Substitutes, Poultry, and Seafood
  • Well-cooked meats, such as pork, beef, lamb, chicken, and turkey (see Food Safety Guidelines for cooking temperatures)
  • Cooked tofu (cut into 1 inch cubes and boiled for at least 5 minutes) or pasteurized tofu
  • Cooked fermented products including miso and tempeh
  • Bacon that is crisp and made at home
  • Hotdogs cooked at home until steaming hot
  • Commercially prepared deli meats sold in a sealed package, such as salami, bologna, ham, turkey, and other deli meats that are cooked until steaming hot (throw away within 48 hours of opening)
  • Thoroughly cooked fish and other seafood, including shrimp, lobster, crab, canned tuna, and canned salmon
  • Canned meats (beef, pork, lamb, poultry, fish, shellfish, game, ham, bacon, sausage, and hot dogs)
  • Canned and shelf-stable smoked fish (refrigerate after opening)
  • Undercooked or raw meats, poultry, and fish, including rare or medium-rare items
  • Raw miso products
  • Raw tempeh
  • Freshly sliced deli meats and meats from street vendors
  • Hard-cured salami in natural wrap
  • Beef jerky
  • Raw shellfish, raw fish (including caviar), sashimi, sushi, and ceviche (“lemon-cooked” or cured fish)
  • Raw or cooked clams, mussels, and oysters
  • Smoked seafood, such as salmon or trout labeled as “Nova style,” “lox,” “kippered,” “smoked,” or “jerky” (unless cooked to 160° F or contained in a cooked dish or casserole)
  • Refrigerated pâtés and meat spreads
and Vegetables
  • Well-washed and peeled raw fruits and vegetables
  • Cooked and canned fruits and vegetables
  • Cooked frozen fruits and vegetables
  • Well-washed and peeled thick-skinned fruits without bruises, such as citrus fruits, bananas, cucumbers, and melons
  • Well-washed and peeled apples (thorough washing is important because slicing through the skin or rind can contaminate the inner fruit)
  • Pasteurized juices and frozen concentrates
  • Commercially packaged dried fruits
  • Shelf-stable bottled salsa (refrigerate after opening)
  • Cooked vegetable sprouts (e.g., mung bean)
  • Fresh, well-washed herbs and dried herbs and spices (added to allowed raw or cooked foods)
  • Unwashed and unpeeled raw fruits, vegetables, or herbs
  • Any fresh or raw fruits and vegetables that can’t be thoroughly washed and peeled or cooked (e.g., blueberries, strawberries, raspberries, cherries, peaches, plums, and grapes that tend to get mold around their stems)
  • Any frozen berries and other thin-skinned frozen fruits
  • Unpasteurized fruit and vegetable juices
  • Fresh fruit salsa or fresh vegetable salsa found in the grocery refrigerator case
  • Vegetarian sushi
  • Unpasteurized items containing raw fruits or raw vegetables found in the grocery refrigerator case
  • All uncooked vegetable sprouts (alfalfa, bean, clover, and all others)
  • All salads from delis or salad bars
  • Boiled well water
  • Tap water and ice made from tap water
  • Commercially bottled distilled, spring, and natural waters
  • Pasteurized fruit and vegetable juices
  • Bottled, canned, or powdered beverages
  • Instant and brewed coffee
  • Hot-brewed teas using commercially packaged tea bags
  • Pasteurized soy milk
  • Commercially made liquid nutritional supplements (e.g., Ensure®, Boost)
  • Unpasteurized eggnog or apple cider and other unpasteurized fruit or vegetables juices
  • Reconstituted protein powder beverages, unless approved by your dietitian
  • Unpasteurized beer (e.g., microbrewery beers and those that are not shelf-stable)
  • Wine
  • Fountain beverages
  • Tea made with loose leaves
Dried Fruits
  • Factory-packaged nuts and dried fruits
  • Roasted nuts from a can or bottle
  • Nuts in baked goods such as peanut butter cookies
  • Commercially packaged nut butters (such as peanut, almond, and soybean)
  • All nuts or dried fruits that are sold open and in bulk, as in some health food or specialty stores
  • Raw nuts
  • Freshly made peanut butter (not commercially packaged)
  • Roasted nuts in the shell
Condiments and
  • Salt and sugar
  • Jellies, syrup, and jams (refrigerate after opening)
  • Pasteurized or flash pasteurized honey
  • Packaged ground black pepper, herbs, and spices added before the cooking process
  • Catsup, mustard, BBQ sauce, and soy sauce, (refrigerate after opening)
  • Pickles, pickle relish, and olives (refrigerate after opening)
  • Vinegar
  • Vegetable oils and shortening
  • Refrigerated margarine and butter
  • Commercially made, shelf-stable mayonnaise and salad dressings, including blue cheese and other cheese-based salad dressings (refrigerate after opening)
  • Cooked gravy and sauces
  • Raw or unpasteurized honey and honeycomb
  • Whole or fresh ground black pepper, unless thoroughly cooked in food
  • Fresh salad dressings (stored in grocer’s refrigerated case) containing raw eggs or cheeses, such as Caesar salad dressing
  • Herbal and nutritional supplement preparations
  • Refrigerated, commercially made, and homemade cakes, pies, pastries, and pudding
  • Refrigerated cream-filled pastries
  • Cookies, both homemade and commercially prepared
  • Shelf-stable, cream-filled cupcakes and fruit pies
  • Candy and gum
  • Unrefrigerated, cream-filled pastry products (not shelf stable)
Eating Outside the Home and Take-Out
  • All foods recommended in previous food groups must come directly off the grill or stove and not be served on steam tables or stored under heat lamps (e.g., freshly made pizza not sliced or reheated, hamburger directly off a grill, just-cooked French fries)
  • Single-serving condiment packages (no pump serve containers)
  • Any food that is not freshly made to order
  • Unpasteurized fruit juices and dairy products (e.g., juice bar establishments such as Jamba Juice®)
  • Raw fruits and vegetables served at salad bars and desserts with fresh fruit
  • Deli meats and cheeses
  • Buffets/smorgasbords
  • Potlucks and sidewalk vendors
  • Soft serve ice cream and yogurt
  • Fast food (e.g., McDonalds®, Subway®)
  • Reheated foods

Always remember: when in doubt, throw it out!

Eating out at restaurants

You can eat out while on a low-microbial diet (as long as you are not a stem cell transplant patient, see guidelines below), as long as you choose the restaurant carefully. Local health departments inspect restaurants to make sure that they are clean, and that they follow safe food practices. You can find out how your local restaurants did on a recent health inspection by going to your local Department of Health (DOH) website. To find out about restaurants in New York City, go to the following website:

You can also ask your local restaurants about their food safety training rules. When you go out to eat, follow the guidelines below.

  • Order all foods to be fully cooked and meats to be well done.
  • Don’t order foods that may have raw eggs (e.g., Caesar salad dressing and hollandaise sauce).
  • Ask the waitstaff if you are not sure of the ingredients in your meal.
  • Don’t eat foods from buffets and salad bars.
  • Ask that your foods be cooked fresh and not served from steam tables or stored under heat lamps.
  • Ask for single-serving condiments, such as catsup and mustard packets. Open containers may be used by many customers.
  • Don’t eat soft serve ice cream and soft serve frozen yogurt. The dispensers may not be cleaned on a regular basis.
  • Always order a whole or personal pizza. Don’t order individual slices, since they are often stored under heat lamps.

Guidelines for bone marrow and stem cell transplant patients

Allogeneic and autologous stem cell transplant patients should not eat out at restaurants for the first 100 days post transplant. Please speak to someone on your healthcare team if you have any questions or concerns about eating out before or after the 100-day period.

Avoid herbal supplements

Don’t take homeopathic remedies or herbal products (e.g., traditional Chinese medicines). Because there are no federal standards for these products in the United States, the way they are processed and stored may pose a health risk. Microbes in these items can also cause an infection. Also, the products themselves could interfere with or change the activity of a prescription medication.

Safe drinking water

Never drink from lakes, rivers, streams, springs, or wells.

If you are unsure if the tap water is safe, check with the local health department or boil or filter the water. Drink bottled water if you think the tap water may not be safe.

If you use well water, you must boil it.  Bring the water to a rolling boil for 15 to 20 minutes. Store boiled water in the refrigerator. Throw away any boiled water that you did not use in 48 hours.

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United States Department of Agriculture (USDA) Food Safety and Inspection Service

US Department of Health and Human Services (USDHHS) Food Safety Information

USDHHS Food and Drug Administration (FDA)

Centers for Disease Control and Prevention Food Safety

Fight BAC! Partnership for Food Safety Education

USDA “Ask Karen” (web-based question and answer system)

NYC Department of Health and Mental Hygiene Restaurant Inspection Information

FDA (toll-free numbers)

(888) SAFE-FOOD (723-3366)

(888) INFO-FDA (463-6332)

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