Aim We examined the difference between the effects of olanzapine (OLZ) and risperidone (RIS) on PR and QT intervals among patients with stable schizophrenia using a cohort analysis. Methods Twenty-one subjects treated with OLZ were enrolled in the study. Following baseline assessments, which included PR and QT intervals, OLZ was switched to RIS for each subject. The same parameters were evaluated following the switch to RIS. Results All patients who had been treated with OLZ were successfully switched to RIS. In all patients, we observed a significant decrease in PR interval (t=2.397, P=0.029) and no change in either QTc or RR interval. In female patients, the QTc interval was significantly decreased (t=3.495, P=0.008) following the switch, while in male patients, the QTc interval did not change. No patients showed a PR interval of >200ms or a QTc interval of >500ms. Conclusion OLZ treatment has a greater prolonging effect on PR and QT intervals compared with RIS. Careful attention may need to be paid to the cardiac conduction system in addition to QT prolongation during OLZ treatment.