After the identification of HIV-2 in 1986, most of the cases reported have been concentrated in West Africa. We identified a case of HIV-2 infection in São Paulo, Brazil of a 45-year-old female who presented with Pneumocystis carinii pneumonia, with a CD4 count of 22 cells/ml. DNA samples from this patient were subjected to end-point PCR amplification of the LTR region. Clones were sequenced and subjected to phylogenetic analyses. All clones were subtype A related, and four presented an insertion, corresponding to an extra NF-kappaB site. This is the first confirmed case report of an HIV-2-infected subject identified in Brazil whose transmission occurred within the country. Furthermore, the NF-kappaB duplication would potentially be associated with an increase in viral cytopathogenicity. This raises concern for the need for permanent monitoring of the spread of HIV-2 in different areas of the world, even considering its lower rate of transmission and pathogenicity when compared to HIV-1.