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We aimed to identify the effect of positive stool cultures (PSCs) on the clinical outcomes of patients undergoing haploidentical hematopoietic stem cell transplantation (haplo-HSCT) (n =332).PSCs were observed in 61 patients (PSC group,18.4％).Enterobacteriaceae in stool specimens was associated with a higher risk of bloodstream infection,and Candida in stool specimens was related to a higher risk of platelet engraftment failure.The cumulative incidence of infection-related mortality 1 year after haplo-HSCT in the PSC group was higher than that of the patients who showed persistently negative stool cultures (NSC group;19.2％ vs.8.9％,P =0.017).The probabilities of overall survival (71.4％ vs.83.8％,P =0.031) and disease-free survival (69.6％ vs.81.0％,P =0.048) 1 year after haplo-HSCT for the PSC group were significantly lower than those for the NSC group,particularly for patients who had Candida in their stool specimens.In multivariate analysis,Candida in stool specimens significantly increased the risk of mortality and was associated with poorer survival.Our results showed that PSC influenced the clinical outcomes after haplo-HSCT,particularly those who had Candida in their stool specimens.