- Introduction: Low Apgar scores (< 7) measured at age 5 minutes can predict short-term infant morbidity and mortality. Although an association exists between low Apgar scores and neuropsychological disorders, other childhood disorders were not thoroughly studied. We aimed to study the possible association between low 5-minute Apgar scores in term newborns and their long-term childhood gastrointestinal (GI) morbidity. Methods: A population based cohort analysis was performed comparing total and different subtypes of GI related pediatric hospitalizations among newborns with normal (≥ 7) and low (< 7) 5-minute Apgar scores. The analysis included all term singletons born between the years 1999–2014 at a single tertiary Regional Medical Center. Infants with congenital malformations, multiple gestations, and all perinatal deaths were excluded from the analysis. GI related morbidities included hospitalizations involving a predefined set of ICD-9 codes, as recorded in the hospital computerized files. A Kaplan-Meier survival curve was constructed to compare the cumulative GI morbidity, and a Cox proportional hazards model was used to adjust for confounders. Results: The study population, including 223 244 term singletons, was followed for an average of 10.02 ± 6.0 years (0–18 years, median 10.25) following discharge from birth hospitalization. Low 5-minute Apgar scores were recorded in 585 (0.3%) newborns. Incidence of GI related hospitalizations was higher among the low versus the normal 5-minute Apgar score group (7.4 versus 5.2%; 8.6/1000 person years (PY) versus 5.2/1000 PY respectively; p = 0.02; odds ratio = 1.66, 95% CI 1.36–1.96). The association remained significant and independent while adjusting for gestational age, fetal weight, offspring gender, maternal age, maternal smoking, hypertension and diabetes (Adjusted HR = 1.57, 95%CI 1.16–2.12, p= 0.003). Conclusions: Low 5 minutes Apgar score is associated with an increased risk for long-term pediatric GI morbidity of the offspring. Our results suggest that Apgar scores can be used as a possible predictor for long-term pediatric morbidities and thus may necessitate appropriate surveillance in this vulnerable group of children.