The lack of the recovery of CD4 T-cells (CD4 recovery) among immunodeficiency virus (HIV)-infected patients on antiretroviral therapy (ART) is not well known. We aimed to analyze the association between single nucleotide polymorphisms (SNPs) underlying vitamin D metabolism and the CD4 recovery in naïve HIV-infected patients who started ART with low baseline CD4 . We conducted a retrospective study in 411 naïve individuals with plasma HIV load >200 copies/mL and CD4 <200 cells/mm . During 24 months of follow-up, all patients had plasma HIV load <50 copies/mL. DNA genotyping was performed using the Sequenom MassARRAY platform. The outcome variable was the change in CD4 during the study. CD4 recovery was higher in patients carrying rs7041 AA genotype (AA versus CC/AC) and rs3829251 AA genotype (AA versus GG/AG) ( -value < 0.05). rs7041 AA genotype was linked to increase in CD4 (adjusted arithmetic mean ratio (aAMR) = 1.22; -value = 0.011), increase in CD4 ≥P75th adjusted odds ratio (aOR) = 2.31; -value = 0.005, slope of CD4 recovery (aAMR = 1.25; -value = 0.008), slope of CD4 recovery ≥ P75th (aOR = 2.55; -value = 0.005) and achievement of CD4 ≥500 cells/mm (aOR = 1.89; -value = 0.023). Besides, rs3829251 AA genotype was related to increase in CD4 (aAMR = 1.43; -value = 0.031), increase in CD4 ≥P75th (aOR = 3.92; -value = 0.030), slope of CD4 recovery (aAMR = 1.40; -value = 0.036), slope of CD4 recovery ≥ P75th (aOR = 3.42; -value = 0.031) and achievement of CD4 ≥500 cells/mm (aOR = 5.68; -value = 0.015). In summary, rs3829251 and rs7041 polymorphisms were associated with CD4 recovery in HIV-infected patients who started cART with low CD4 T-cell counts.