Hospital average length of stay varies considerably between countries. However, there is limited patient-level research identifying or discounting possible reasons for these differences. This study compares the length of stay of patients in Japan, where it is the longest in the OECD, and Canada, where length of stay is closer to the OECD mean. Administrative patient-level data, including age, gender, co-morbidities, intervention, discharge plan, outcome and length of stay were collected from two Japanese and two Ontario, Canada hospitals for two diagnoses: colorectal cancer surgery and acute myocardial infarction. Analyses examined linkages between patient characteristics, hospitals and countries and length of stay. When controlling for patient demographic characteristics, the incidence of co-morbidities and discharge plan practices, Japanese length of stay tended to be significantly longer than that in Canada for both diagnoses. Mortality rates were not significantly different; however, the readmission rate (28 days or less) for acute myocardial infarction was higher in the Canadian hospitals. The findings indicate that non-clinical factors contribute to sustained international differences in length of stay. These factors may include professional or cultural norms, differing payment schemes and access to long-term care facilities. The study also introduces a protocol that can be used for international patient-level comparisons that can enable effective policy and management learning.