Genes located on the CTX element and the Vibrio cholerae pathogenicity island (VPI) were investigated in 297 clinical V. cholerae O1 and 76 environmental O1 and non-O1 isolates from Brazil between 1991 and 1999. RAPD analysis suggested that serogroup O1 strains regardless of clinical or environmental source were clonal while non-O1 strains showed greater diversity. PCR analysis showed that 71% of O1 clinical isolates had a complete set of CTX element target genes (ctxA, ctxB, zot and ace) and 68% a complete set of the VPI genes studied (orf1, aldA, tagA, tcpA, toxT and int genes). The results also showed that 72.4% of environmental O1 isolates possessed ctxA, ctxB, zot and ace genes while environmental non-O1 strains rarely possessed virulence genes. Our data are consistent with the hypothesis that the CTX element and the VPI can have a mosaic structure in some V. cholerae strains, genotype diversity is due to the circulation of virulence genes which are more commonly found in O1 strains in Brazil. This study also shows that the aquatic environment is a potential source for virulence genes and toxigenic V. cholerae during epidemic periods.