A methodological approach to infant mortality estimation in Brazil based on vital information provided by Ministry of Health systems is presented. The study evaluated the available data to establish criteria for identifying municipalities with serious data deficiencies, proposing an adequacy index. All municipalities were classified in strata according to geographic region and adequacy of information. To estimate infant mortality by macro-geographic region, in 1998, direct calculation was performed in strata with adequate information. The United Nations model was used in the other geographic strata. The Brazilian North presented the most deficient information, with 63% of the municipalities presenting inadequate reporting (35% of the regional population), followed by the Northeast (29% of the population). In the South, only 1% of the population showed inadequate information. For the whole country, 12% of the population presented serious problems in completeness of death reports. The adequacy index varied from -28% in Maranhão to 94% in Rio de Janeiro. The infant mortality rate was estimated in the interval 30.7-32.6 per 1,000 live births and the completeness of infant deaths from 61.8% to 65.6%.