Objectives The Korea HIV/AIDS cohort was constructed with 18 hospitals that care for HIV-infected individuals in 2006. We compared the epidemiological and immunological characteristics of the cohort registrants with those of the HIV-infected population at the time of HIV diagnosis. Methods This study was conducted on 5717 people living with HIV/AIDS from 1985 to 2009, of which 789 individuals registered with the Korea HIV/AIDS cohort study. Individuals who had data from initial CD4+ T-cell counts measured within 6 months following HIV diagnosis were selected as study participants to predict the status of disease progression at the time of HIV diagnosis. A total of 2886 patients (50%) were selected from people living with HIV/AIDS, of whom 424 individuals (54%) were cohort registrants. The χ2 test and Wilcoxon rank sum test were used for analysis. Results The distributions of age, marital status, diagnosed regions, reason for HIV testing, and screening site were similar between the HIV-infected population and the cohort registrants. In 1985–2004, the male ratio for the cohort registrants (94.3%) was significantly higher than that measured for the HIV-infected population (89.5%) (p = 0.0339). With regard to transmission route, homosexual contact of cohort registrants (46.6%) was higher than that of the HIV-infected population (40.1%) (p = 0.022) in 2005–2009. No statistical difference in CD4+ T-cell counts at the time of HIV diagnosis was found between the HIV-infected population and cohort registrants (p = 0.2195). Conclusion The Korea HIV/AIDS cohort registrants represent the HIV-infected population, and the data collected from this cohort could be used as a foundation for national statistics.