Hirschsprung disease (HD; also known as congenital aganglionic megacolon) affects 1 in 5000 live births [2]. Surgical repair (excision of the aganglionic colon and pull through of the normally ganglionated intestine to the anal canal) is typically performed in infants with HD during the first few months of life [3, 4]. A subgroup of these children with HD will also develop Hirschsprung associated enterocolitis (HAEC), a potentially severe infection of the small bowel and colon[5]. Children who develop HAEC can present with fever, abdominal distention, explosive diarrhea, vomiting, lethargy, and if not diagnosed and treated promptly, can lead to life threatening sepsis and death. HAEC may occur pre- or post-surgery in HD patients. There have been widely varying reports of HAEC incidence ranging from 15-50% pre-surgery to 2-30% post-surgery. A lack of clear definition of HAEC criteria is at least partially responsible for this significant variation in reported incidence[6, 7]. A standardized definition of HAEC was recently developed and published in 2009[1]. The HAEC score consists of the most important clinical diagnostic criteria for HAEC identified from a group of international experts using the Delphi method. Preliminary validation with case scenarios was achieved and the HAEC score can now be used as a standardized and reproducible outcome measure for future studies on children with Hirschsprung disease. Now it is possible to perform rigorous studies of the genetic, immune, and microbial differences in HD patients who develop HAEC compared with those children with HD that have not developed HAEC.