The location of midgut bacteria relative to meconial peritrophic membranes (MPMs) and changes in bacterial numbers during midgut metamorphosis were studied in Anopheles punctipennis (Say), Culex pipiens (L.), and Aedes aegypti (L.) pupae and newly emerged adults. After adult emergence in Aedes, Anopheles, and most Culex, there were few to no bacteria in the midgut. In most newly emerged adult mosquitoes, few bacteria were found in either the lumen or within the MPMs/meconia. In a few Culex specimens, high numbers of bacteria were found in the MPMs/meconia and low numbers in the lumen. In all three species bacterial counts were high in fourth instars, decreased after final larval defecation, increased in young pupae, and increased further in old pupae. A very effective gut sterilization mechanism is operating during mosquito metamorphosis and adult emergence. This mechanism appears to involve the sequestration of remaining larval gut bacteria within the confines of the meconium and one or two MPMs and the possible bactericidal effect of the exuvial (molting) fluid, which is ingested during the process of adult emergence.