Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is characterized by hypoperistalsis in the presence of ganglion cells, malrotation, microcolon, bladder distension, and female predilection. We draw attention to the long-term management of a patient with MMIHS and propose a pathogenetic mechanism to account for this syndrome. We propose that the initial event in the pathogenesis of MMIHS is an intramural inflammatory process that affects the gastrointestinal and urinary tracts. This leads to extensive fibrosis which destroys the intestinal neural network, producing hypoperistalsis. The same process causes neuromuscular incoordination in the bladder wall, resulting in irregular bladder contractions against a "closed sphincter" leading to bladder distension. The enlarged bladder then interferes with the rotation of the intestine causing malrotation.