In Gli^J29-41bl homozygous embryos, tracheal phenotypes are apparent from stage 15. At stage 16 in these embryos the average dorsal trunk length is significantly greater than wild type (P<0.005) (146+/-6% mean+/-s.e.m., n>5, normalized to stage 16 wild-type value). These embryos have only mild diameter increases in the dorsal trunk and other primary tracheal branches, and no loss of lumen in ganglionic branches. Unlike wild-type, post stage 15 trachea in Gli^J29-41bl homozygotes are unable to exclude from their lumens, a fluorescently labelled 10kDa dextran injected into the body cavity. This is consistent with these trachea lacking a functioning septate junction barrier.