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The predictive factors of negative outcome in initial i.v. atropine (IA) therapy of infantile hypertrophic pyloric stenosis (IHPS) are unknown. Conservative therapy for IHPS is useful for infants because it does not have the risk of surgical and anesthetic stress, but some cases of atropine therapy result in failure. This study clarified the predictive markers of negative outcome in initial atropine therapy for IHPS.Seventy-six patients with IHPS admitted from 1998 to 2011 were included in this study. The predictive risk factors of negative outcome in initial atropine therapy for IHPS were evaluated.Thirty-one patients initially underwent non-operative therapy for IHPS during the study period. Of the 31 patients, 18 (58%) ceased projectile vomiting (PV) with IA and subsequent oral atropine. Univariate analysis showed that lack of bodyweight gain before treatment, elevated urine potassium at admission, and PV occurring ≥5 times (PV ≥5) in total for 3 days from IA initiation were predictive risk factors for negative outcome in IHPS. Multivariate analysis identified only PV ≥5 in total for 3 days after IA initiation as independently associated with failure of atropine for IHPS.PV ≥5 in total for 3 days after IA initiation is a potential indicator of negative outcome of IA in IHPS patients. The present results provide valuable information for determining whether early surgical intervention for IHPS or initial atropine therapy is the best option.