Apart from the risk posed by eating the decaying food they were laid in, eating the eggs of most fly species is generally no more harmful to healthy adults than eating other organic matter. Some species of fly, however, are capable of either hatching out or surviving passage through the human gastrointestinal tract, according to the Centers for Disease Control and Prevention, and can cause unpleasant symptoms if an infestation occurs.
Fly infestation of the body is known as myiasis, and several species of fly are able to infect humans, the CDC reports. In one case, a 1-year-old girl in Washington state was brought to her doctor when her mother saw "moving worms" in the girl's feces. These turned out to be maggots of the species Muscina stabulans, or false stable flies, that infested the girl's GI tract after she was fed overripe bananas containing the unhatched fly eggs. As reported by her doctor, the girl was asymptomatic and the issue cleared up without treatment.
Sometimes, however, internal myiasis brought on by ingesting fly eggs causes cramps, vomiting and diarrhea. The CDC advises covering exposed fruit and washing fruits and vegetables thoroughly before consumption. Deliberately eating fly eggs is also not advisable for most people.