Hirschsprung's-associated enterocolitis (HAEC) continues to be a significant source of morbidity for patients with Hirschsprung's disease (HD). New clinical and histologic classification systems for HAEC will improve consistency between reports and increase the ability to compare outcomes. A complete understanding of disease pathogenesis is lacking, but evidence suggests that the intestinal microbiota may play a role in the development of HD and HAEC. The benefits of adjunctive therapies, such as anal dilations and botulinum toxin to reduce the incidence of HAEC following corrective endorectal pull-through, remain controversial. Finally, new clinical data have identified an association between HAEC and inflammatory bowel disease and will likely lead to further genetic studies to elucidate the connection between these two disease processes.