With the aim of evaluating gender differences in one of the poorest districts of Buenos Aires, we reviewed epidemiological and clinical data of newly-diagnosed HIV patients at the Diego Paroissien Hospital between 1998 and 2005.We analyzed 524 clinical charts, 329 (62.8%) of which were from the 1998 to 2002 period and 195 (37.2%) from 2003 to 2005. Women accounted for 241 (46%) of the patients. The dominant mode of transmission was sexual intercourse in women and intravenous drug-use in men. At the time of diagnosis, women were at a significantly lower clinical stage, were younger, and had higher CD4 counts and lower viral loads. No gender differences were found in the rates of continued clinical care or continued antiretroviral therapy at one year follow-up. Comparing the periods 1998 to 2002 and 2003 to 2005, there was a statistically significant increase in diagnoses made during the pregnancy screening in women, in sexual transmission as the primary route of HIV infection, in the frequency of patients (both men and women) who had continued clinical care at one year follow-up, and a decreasing of intravenous drug-use in both sexes.The observed gender differences in the 2003-2005 period persisted even when those women who were diagnosed during their pregnancy screening were excluded from the analysis.