The aim of this work was to compare thymic function-related markers for predicting early CD4 T-cell repopulation in adult HIV-infected patients under HAART. Forty-three consecutive antiretroviral-naive patients were prospectively analysed for clinical, biochemical, immunological and virological parameters at starting HAART, and followed for 4 weeks and every 12 weeks thereafter. At baseline, all patients underwent a thoracic computer tomography scan, in order to measure thymic volume, as well, T-cell phenotype (naive CD4 and CD8 T cells) and the number of TREC-bearing cells were obtained. CD4 cell repopulation was considered as an increase ≥200 cells/mm³ above baseline count. Twenty-seven patients (62.8%) increased ≥200 cells/mm³ above baseline levels during the follow-up. The median time to event was 182 days (84–537 days). On the univariate analysis, to be younger than 36 years, showing a CD4 cell count ≥272 cells/mm³, a total naive T-cell count ≥128 cells/mm³, a TREC-bearing cell count ≥0.74 cells/mm³, and a thymic volume ≥3.07 cc at baseline were statistically associated to the event studied. However, when the multivariate analysis was performed, only thymic volume at baseline was independently associated (P=0.002) to CD4 cell recovery. This co-variable was identified as a positive predictor [hazard ratio, 1.22 (95% confidence interval: 1.16–1.28)]. In summary, data presented herewith show that thymic volume is the best thymic function-related marker for predicting early CD4 T-cell recovery in adult HIV-infected patients under HAART.