To evaluate the recombination profiles and evolutionary history of HIV-1 BC recombinants in Southern Brazil, 81 isolates collected in the city of Porto Alegre (Rio Grande do Sul State) from 1998 to 2006 previously subtyped as C (env-gp120/C2V3) were screened in the protease-reverse transcriptase (pr/rt), integrase and gp41 genomic regions. Detailed phylogenetic, bootscan and informative site analyses were performed to trace the subtype classification. The evolutionary rate and divergence time of the Brazilian CRF31_BC epidemic were estimated using a Bayesian Markov Chain Monte Carlo framework. Analysis of the four target regions identified: 43 isolates as "pure" subtype C, 23 as CRF31_BC, and 15 as unique BC recombinant forms (URFs_BC). Recombination breakpoints were mainly localized in the rt gene and 100% of the recombinant samples could be detected analyzing only this region. Most URFs_BC (86.7%) contained small subtype B fragments (<or=160nt) in the rt region and shared one of the recombination breakpoints with CRF31_BC. In conclusion, despite the high co-prevalence of subtypes B and C in Porto Alegre, the diversity of BC recombinant forms circulating in this region was extremely low. Most BC recombinants were CRF31_BC and URFs_BC that appeared to be second generation recombinants derived from CRF31_BC and subtype C strains, confirming the importance of this CRF in this region. The emergence of the CRF31_BC was estimated to be around 1988 (1982-1992).