Brevibacillus laterosporus is a sporulating bacteria, with typical canoe-shaped parasporal bodies attached to the spores. It has shown great biotechnological potential, including its broad pathogenic spectrum against different orders of insects and other invertebrates with medical-veterinary-sanitary importance. The high degree of synanthropy of muscoid dipterans and the damage they cause being a source of myiasis and carriers of pathogens encourage research into their population control. The objective of the study was to evaluate the histopathological effects caused by B. laterosporus NRS 590 on larvae and adults of M. domestica and C. megacephala. The flies were collected in garbage dumpsters, identified and the respective colonies were adapted to laboratory conditions (air-conditioned chamber with regulated humidity and temperature). Different concentrations of bacterial spore suspensions were offered to neo larvae and adults. Larvae and adults were dissected and intestinal epithelial cells of the flies, in temporal kinetics, were demonstrated using transmission electron microscopy (TEM) techniques. Irregular microvilli were observed in the intestines of both adult and larvae tested after 6 h of treatment. At 12 h and 24 h, intense cellular disorganization was observed and at 24 h and 48 h there was discontinuity of microvilli, cell extrusion and nuclear damage in some cells, as well. Spores of B. laterosporus NRS590 produce histopathological effects on both larvae and adults of synanthropic flies, being an alternative active principle in eco-friendly insecticides.