1. The molecular basis of hemophilia B was investigated in 19 Brazilian patients from 14 unrelated families. 2. Southern blotting of TaqI-digested DNA samples was employed for the screening of gene lesions followed by polymerase chain reaction and DNA sequencing for the characterization of mutations. 3. Three different gene mutations were characterized: a nonsense mutation at nucleotide 30875 (codon 252, CGA-->TGA), a partial deletion comprising exons 1-3 (at least 7.4 kb of extension), and a complete deletion (at least 42 kb of extension). These patients are now referred to as Ribeirão Preto 1, Ribeirão Preto 2 and Ribeirão Preto 3, respectively. 4. The factor IX haplotype (composed of 7 polymorphic sites) associated with each mutation was determined. Comparisons with previous studies confirmed an independent origin for the nonsense mutation. 5. This study represents the first survey of gene lesions associated with hemophilia B in South America. The results indicate the presence of heterogeneous mutations, as observed in other populations. These results also contribute to the understanding of the mechanisms involved in the mutations affecting the FIX gene.