BACKGROUND: This study is to investigate the association between the distribution of multimorbidity and length of stay and medical expenses among inpatients in a municipal hospital to achieve an integrated care setting. METHODS: We used the exploratory factor analysis and the generalized estimating equation model to analyze the data from patients living in the northeast region of Seoul, who were hospitalized from January 2017 to December 2017 in a municipal hospital. RESULTS: As a result of the factor analysis, seven types of multiple chronic diseases were classified. Among the elderly patients admitted to municipal hospitals, the burden of medical expenses was mainly influenced by the length of stay (B=310,719, p-value<0.0001), not the type of disease (all not significant). Length of stay were mainly due to psychiatric illness (factor 1: B=4.323, p-value<0.0001) related to the brain and metabolic diseases (factor 2: B=2.364, p-value=0.003). CONCLUSION This study showed that the medical expenses of the elderly patients were largely due to prolonged hospitalization, not multimorbidity. Therefore, it is necessary to develop an integrated care paradigm strategy cope with the multimorbidity of the elderly in the community and to alleviate the socio-economic burden.