Aim: The purpose of this study was to explore the impact of attributes of medical care organizations and patients on medical resource utilization by hemophilia (hemophilia A and hemophilia B; Hemophilia with musculoskeletal system and without). Methods: Hospitalization due to hemophilia (ICD9: 286.0 and 286.1) and hemophilia with musculoskeletal system (ICD9: 710.xx-739.xx) between 2001 and 2010 were identified from a national health insurance database. Calculated by patients and hospital characteristics, length of hospital stay, medical cost of hospitalization was analyzed. Results: Of the total of 2150 patients, a systemic analysis of the results showed a mean patient age of 30.2 and average medical costs per patient of NT $672,335 (US $21,010). We found the mean cost of cases being significantly higher during the hemophilia A that in the hemophilia B (NT $708,620 vs. NT $422,322, P < 0.001), and medical costs such as those for hemophilia with musculoskeletal system (NT $1,419,158) were significantly higher than comparison patients (NT $463,889) (P < 0.001). Conclusions: Taiwan operates a national insurance global budget payment system. Healthcare system budgetary pressures are exacerbated by increases in the costs of hemophilia treatment. Suggesting that Bureau of National Health Insurance (BNHI) should consider establishing official primary and secondary prophylaxis treatment and dose regimen (such as dose or tailored-dose) should consider establishing a more aggressive and comprehensive standard of care for hemophiliacs. It is believed that that will have a significant impact on future treatment for hemophiliacs in Taiwan.