“Immunological discordance,” i.e., immunological failure despite complete viral suppression in human immunodeficiency virus (HIV)-infected patients receiving antiretroviral therapy (ART), is associated with increased risk of AIDS or death. To evaluate risk factors for immunological discordance in a resource-limited setting in which patients usually present late with low CD4 cell counts, we conducted a case-control study among HIV-infected patients receiving ART and having undetectable HIV RNA. The study included patients with immunological discordance (cases), which was defined as CD4 cell count < 30% above baseline and absolute CD4 cell count < 200 cells/mm³ at the first 12 months of undetectable HIV RNA (<50 copies/mL). Patients without immunological discordance were included as controls. Of 142 patients (44 cases; 98 controls), the mean age was 38.6 ± 9.4 years and 67.6% were men; 65.5% had history of opportunistic infections. In multivariate analysis, only baseline CD4 cell count < 100 cells/mm³ (odd ratio [OR], 2.53; 95% confidence interval [CI], 1.04–6.14; P = 0.040) and history of lost to follow-up (OR, 11.04; 95% CI, 2.87–42.46; P < 0.001) were significantly associated with immunological discordance. Early initiation of ART and intervention to improve regular clinic visit compliance and adherence to ART are crucial to prevent immunological discordance among HIV-infected patients.