The findings of a study published in the European Journal of Gastroenterology & Hepatology suggested that neonatal constipation is associated with long-term gastrointestinal (GI)-related disorders and should be considered clinically significant even when the diagnosis of Hirschsprungs disease (HD) is excluded. The present study aimed to describe the long-term clinical outcomes of neonates with a clinical suspicion of HD which was excluded by rectal suction biopsy. This was a single-center double-cohort comparative study, wherein neonates who underwent rectal mucosa biopsy for suspected HD were age and sex matched with healthy controls. A survey was conducted on clinical outcomes, stooling patterns, and other GI-related conditions. Overall, 51 neonates were included comprising 25 cases and 26 controls, of which 41% were males, and their median time of follow-up was 4.25 years. It was found that 36% of patients in the case group required prolonged laxative use for constipation during their first year of life, whereas none of the controls required prolonged laxative use. Furthermore, this difference was maintained at the end of follow-up, with 20% versus 0%, respectively. In addition, neonates in the case group were significantly more likely to be hospitalized or to be diagnosed with a chronic GI-related condition than those in the control group. Thus, it was stated that neonates with early-onset abnormal stooling patterns should be monitored with adequate pediatrician or pediatric gastroenterologist follow-up.