Although there is a chance fruit flies can carry germs on to your food, this is not very likely. Fruit flies are annoying, but they probably will not hurt you. Because they are such a nuisance, however, most people want to get rid of these pesky bugs as quickly as possible. Some people use pesticid sprays on the fruit flies. Although this will kill the flies, it will also spread harmful poison all over your kitchen. Luckily, there is also a completely safe way for you to get rid of fruit flies in your house. The first step is for you to remove all fruits or vegetables from your counter. Store these items in the refrigerator or in sealed containers. Clean up any spilled juice or bits of food that might be on the floor. Take out the trash and empty the recycling bin. Wash any dirty dishes that are in your sink. Doing all of these things will stop new fruit flies from finding food or places to lay their eggs.