Green fluorescent protein-producing Escherichia coli were used to investigate the fate of bacteria in the alimentary tract of sterile grown maggots, Lucilia sericata (Meigen), using a laser scanning confocal microscope. A computer program was used to analyze the intensity of the fluorescence and to quantify the number of bacteria. The crop and the anterior midgut were the most heavily infected areas of the intestine. A significant decrease in the amount of bacteria was observed in the posterior midgut. The number of bacteria decreased even more significantly in the anterior hindgut and practically no bacteria were seen in the posterior end, near the anus. The viability of bacteria in the different gut sections was examined. It was shown that 66.7% of the crops, 52.8% of the midguts, 55.6% of the anterior hindguts, and 17.8% of posterior hindguts harbored living bacteria. In conclusion, during their passage through the digestive tract the majority of E. coli was destroyed in the midgut. Most of the remaining bacteria were killed in the hindgut, indicating that the feces were either sterile or contained only small numbers of bacteria.