The study aimed to compare the gender difference in clinical manifestations at time of HIV diagnosis and after one year of antiretroviral therapy, and to determine the influence of gender on HIV care continuity. A retrospective study was conducted using chart review of adults diagnosed with HIV infection from 1993-2008 at a university-affiliated AIDS-designated hospital in Taiwan. Men who acknowledged having sex with men were excluded in order to compare the gender differences among patients with similar routes of HIV transmission and social context. Of the 682 patients with HIV, 86.6% were men. There were no significant gender differences in clinical, immunological or virological parameters at baseline. After one year of antiretroviral therapy, the curves of changes in CD4 cell counts in men and women were parallel over time. Continuity of care, referring to at least one appointment in each six-month window during 2005-2008, was significantly associated with age >50 years (OR = 2.54, 95% CI: 1.04-6.16), being enrolled in the case management programme (OR = 4.93, 95% CI: 2.53-9.62), acquisition of HIV via heterosexual contact (OR = 3.63, 95% CI: 1.38-9.55), CD4 lymphocyte count <200 counts/mm(3) at baseline (OR = 3.09, 95% CI: 1.38-6.96), being on highly active antiretroviral therapy (OR = 4.77, 95% CI: 2.37-9.59), and with sero-discordant partners (OR = 2.51, 95% CI: 1.07-5.87). The findings indicate that gender does not appear to be associated with HIV disease manifestations and continuity of care. Further research to develop optimal methods to retain patients in HIV care is needed.