Background The transgender population is highly affected by STI and HIV epidemic, with high stigma and social discrimination. In Paraguay there is a lack of information concerning HIV and syphilis prevalence in this population. Generally, data on this population is mixed with that of men who have sex with men (MSM). It is estimated there are 421 transgender citizens throughout the country.

Methods Cross sectional observational study at subnational level, that included a survey and linked confidential serological tests from August to September 2011. HIV and syphilis were screened with rapid tests. HIV was confirmed with Western Blot and syphilis with TPHA for those reactive. The study population was people of male sex at birth that self-identify as females, with or without modification of their body and clothing according to said identity. A mapping of transgender was carried out, and subsequently the study was offered to all mapped people in the geographical areas of Capital, Itapúa, Caaguazú, Paraná and Amambay.

Results 311 transgender participated in the study, 237 agreed to HIV testing and 247 to syphilis testing. HIV and syphilis prevalence was 27% (IC95% 21–32) and 12% (IC95% 8–16) respectively. HIV/syphilis co-infection occurred in 6% of cases. 89% were sexual workers. The associated risk factors for HIV infection were age, non-injectable drug use and sexual work time (p < 0.05). Among those who tested positive for HIV, 60% were previously known HIV positive and 19% for those not submitted to the test. That data was found through the introduction of personal code in the information system.

Conclusions HIV prevalence is high, similar to other Latin american countries. The prevalence of syphilis and syphilis/HIV co-infection is high. The high prevalence of non-injectable drug use implies the need for changing prevention strategies.