In Iran, the HIV/AIDS epidemic is growing during an era of scaling up the national surveillance system and antiretroviral therapy programs. We examined the early loss to follow-up and mortality rates in a retrospective cohort of 1495 HIV-infected patients by survival proportional hazard Cox model. We also conducted a data abstraction sub-study in a systematic random sample of 147 patients to assess the association between mortality and predictor factors. Overall, 17.3% patients were not seen after their first visit and 17.4% more lost by 6 months. The overall mortality rate was 7.0 (95% CI 6.1–8.1) per 100 person-years. Moreover, crude mortality rate was higher in men (8.6) than in women (1.7), with an age-adjusted hazard ratio for men compared to women of 4.55 (95% CI 2.31-8.93). Lastly, history of tuberculosis and not being on antiretroviral therapy were significantly associated with higher mortality in the patient sub-sample.