OBJECTIVE Studies examining functional outcomes and health-related quality of life for patients with congenital surgical anomalies (CSA) are increasingly common. However, the prevalence of mental health disorders in this population has not been determined. The purpose of this review is to summarize the reported prevalence of mental health disorders in children born with gastrointestinal CSA. METHODS A systematic review of the literature was conducted on Medline (OVID), EMBASE (OVID), CINAHL (EbscoHost), and Scopus to identify studies reporting mental health diagnoses in children with a gastrointestinal CSA. A meta-analysis of the prevalence of anxiety disorders and depressive disorders was completed. RESULTS Of 2546 manuscripts, seven met the inclusion criteria. All included manuscripts looked at patients with anorectal malformation (ARM) and/or Hirschsprung disease (HD). No studies assessed other gastrointestinal CSAs. A total of 183 psychiatric diagnoses were reported in 1167 patients. A pooled analysis of ARM patients revealed a 14.0% prevalence of anxiety disorders (N = 208; CI95 = 4.4-23.4%) and an 18.75% prevalence of depressive disorders (N = 48; CI95 = 7.7-29.8%). A pooled analysis of HD patients revealed a 15.8% prevalence of anxiety disorders (N = 19; CI95 = 0.6-32.2%) and a 4.75% prevalence of depressive disorders (N = 758; CI95 = 3.23-6.26%). CONCLUSIONS There is a paucity of evidence on mental health outcomes of individuals born with gastrointestinal CSA. However, the available evidence suggested a high prevalence of mental health diagnoses in individuals born with ARM or HD with 1 in 7 having an anxiety disorder. Additionally, 1 in 5 ARM patients and 1 in 20 HD patients were diagnosed with a depressive disorder. METHODS Systematic review and meta-analysis. METHODS IV.