This study investigated the association between gastrointestinal symptoms and a broad set of emotional and behavioral concerns in 95 children with high-functioning autism and IQ scores ≥ 80. Gastrointestinal symptoms were assessed via the Autism Treatment Network’s Gastrointestinal Symptom Inventory, and data were gathered on autism symptom severity, adaptive behavior, and multiple internalizing and externalizing problems. The majority (61%) of children had at least one reported gastrointestinal symptom. Emotional and behavioral problems were also common but with a high degree of variability. Children with and without gastrointestinal problems did not differ in autism symptom severity, adaptive behavior, or total internalizing or externalizing problem scores. However, participants with gastrointestinal problems had significantly higher levels of affective problems. This finding is consistent with a small body of research noting a relationship between gastrointestinal problems, irritability, and mood problems in autism spectrum disorder. More research to identify the mechanisms underlying this relationship in autism spectrum disorder is warranted. Future research should include a medical assessment of gastrointestinal concerns, longitudinal design, and participants with a range of autism spectrum disorder severity in order to clarify the directionality of this relationship and to identify factors that may impact heterogeneity in the behavioral manifestation of gastrointestinal concerns.