Our present detailed understanding of the genetic mechanisms controlling segmentation has been made possible, in large part, by comprehensive screens of cuticular morphology that identified genes involved in epidermal patterning. To systematically identify genes involved in internal morphogenesis, specifically development of the gut, we have screened mutant embryos produced by a collection of 53 embryonic lethal mutations affecting embryonic pattern formation or differentiation, and a collection of 161 deficiencies covering, in aggregate, approximately 70% of the genome. Staining with the anti-crumbs antibody was used to characterize the Malpighian tubules and hindgut, as well as other internal organs. The geneshuckebein, tailless andwingless, and two previously undescribed loci at 24C/D and 68D/E, are required to establish the primordia for the posterior midgut and hindgut/Malpighian tubules. A locus in region 30A/C is required for extension of the midgut epithelium to surround the yolk, and region 36E/37F is required for outbudding of the Malpighian tubule primordia. Several deficiencies were identified that uncover loci with specific effects on the morphogenesis (elongation, lumen formation) of the hindgut and Malpighian tubules and on the formation of constrictions in the midgut.