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Background Highly active antiretroviral therapy (HAART) roduces profound suppression of HIV replication, substantial increase in CD4+ T cells, and partial reconstitution of the immune system. However, the numbers of subjects were small in previous Chinese studies. This study evaluated the efficacy and side effects of HAART in Chinese advanced AIDS patients.Methods One hundred and three antiretroviral drug naive AIDS patients were enrolled in this study and were divided into two groups by their baseline CD4+ count: ＜100 cells/ μl or ≥ 100 cells/μl. Clinical, virological and immunological outcomes were monitored at baseline and at 1, 3, 6, 9 and 12 months during the course of treatment with HAART.Results One patient died and another was lost from the follow-up. For the remaining 101 HIV/AIDS patients at the 12th month during the HAART, the plasma viral load (VL) was reduced to (3.2±0.7) lg copies/ml, the CD4+ count increased to (168±51) cells/μl [among which the naive phenotype (CD45RA+CD62L+) increased to (49±27) cells/μl and the memory phenotype (CD45RA￣) increased to (119±55) cells/μl], and the percentage of CD4+CD28+ cells increased. At the same time, there was a significant reduction of CD8+ T cell activation. In the 69 patients with the baseline CD4+ count ＜100 cells/μl, 37 had a VL ＜50 copies/ml; while in the 34 patients with the baseline CD4+ count ≥ 100 cells/μl, 25 had a VL ＜50 copies/ml, the difference between the two groups was statistically significant. The CD4+ T cell count showed a two-phase increase during HAART and a significant positive correlation was shown between the change of CD4+ count and plasma VL. Over 12 months of HAART,10 patients had gastrointestinal side effects, 13 peripheral neuritis, 7 hepatic lesions, 8 hematological side effects,8 skin rashes, 10 lipodystrophy and 1 renal calculus.Conclusions Immune reconstitution as well as the significantly improved clinical outcomes is observed in Chinese advanced AIDS patients after HAART. Side effects are common during HAART and require clinical attention.