OBJECTIVES: To estimate the impact of the use of more detailed direct medical costs for the economic evaluations (EEs) of universal vaccinations against rotavirus and varicella in Brazil on the incremental cost-effectiveness ratios (ICERs). METHODS: Previous published EEs were used as basis and new direct medical costs estimates for rotavirus and varicella were developed, with the inclusion of specific costs of the private health care system (HCS) for the two diseases, inclusion of public participation for dispensing drugs in the case of rotavirus and inclusion of drugs costs in the public HCS in the case of varicella. Cost estimate methods consisted of gross-costing and micro-costing. Data were obtained from national regulatory agency database (ANS), household survey (PNAD), private (CBHPM, TUNEP) and public (Ministry of Health) reference lists. Direct medical costs were then applied to the previous models, preserving  non-medical direct and indirect costs, all costs in 2004 Reals. ICERs were recalculated and compared to the original calculations, from the HCS and societal perspective. Univariate sensitivity analysis was performed to each cost item and discount rate to analyse individual impact on ICER. RESULTS: From the societal perspective, there was an estimated disease total cost increase of 16% for rotavirus and 11% for varicella, as well as increase of savings with the vaccination of 18% and 16%, respectively. ICERs were reduced by 20% for rotavirus (to €292/LYS) and 4% for varicella (to €4098/LYS), still below the threshold (3xGDP per capita). Sensitivity analysis indicated that EEs of vaccination against rotavirus and varicella were more sensitive to the vaccination program cost estimates, especially the vaccine price. CONCLUSIONS: Although the more detailed cost estimates reduced the ICERs, the level of cost-effectiveness of the two vaccination programs remained the same. Sensitivity analysis pointed out the relevance of the vaccine cost comparatively to the direct medical costs.