The hypothyroidism group had the lowest CD4+ cell count (per μL) over the whole 6 years, and it was significantly lower than that of the euthyroidism group in the year HAART started as well as 2 and 4 years after (181.91 ± 135.79 vs. 315.49 ± 177.97, 352.27 ± 142.25 vs. 504.47 ± 199.76, 387.00 ± 170.44 vs. 567.11 ± 205.39, P < 0.05; 461.09 ± 203.43 vs. 586.42 ± 223.93, P > 0.05). This evidence concerns the gene CD4 and hypothyroidism.