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Background CD4~+ T cell counts have been used as the indicator of human immunodeficiency virus type 1 (HIV-1) disease progression and thereby to determine when to start highly active antiretroviral therapy (HAART). Whether and how the baseline CD4~+T cell count affects the immunological and viral responses or adverse reactions to nevirapine (NVP)-containing HAART in Chinese HIV-1 infected adults remain to be characterized.Methods One hundred and ninety-eight HIV-seropositive antiretroviral therapy (ART)-naive subjects were enrolled into a prospective study from 2005 to 2007. Data were analyzed by groups based on baseline CD4~+T cell counts either between 100-200 cells/μl or 201-350 cells/pl. Viral responses, immunologic responses and adverse events were monitored at baseline and at weeks 4, 12, 24, 36, 52, 68, 84, 100.Results Eighty-six and 112 subjects ranged their CD4~+T cell counts 100-200 cells/μl and 201-350 cells/μl, respectively.The pre-HAART viral load in CD4 201-350 cells/μl group was significantly lower than that in CD4 100-200 cells/μl group (P=0.000). After treatment, no significant differences were observed between these two groups either in the plasma viral load (pVL) or in the viral response rate calculated as the percentage of pVL less than 50 copies/μl or less than 400 copies/ml. The CD4~+T cell counts were statistically higher in the 201-350 group during the entire follow-ups (P<0.01) though CD4~+ T cell count increases were similar in these two groups. After 100-week treatment, the median of CD4~+ T cell counts were increased to 331 cells/μl for CD4 100-200 cells/μl group and to 462 cells/μl for CD4 201-350 cells/μl group.Only a slightly higher incidence of nausea was observed in CD4 201-350 cells/μl group (P=0.05) among all adverse reactions, including rash and liver function abnormality.Conclusions The pVLs and viral response rates are unlikely to be associated with the baseline CD4~+T cell counts. Initiating HAART in Chinese HIV-1 infected patients with higher baseline CD4~+T cell counts could result in higher total CD4~+ T cell counts thereby achieve a better immune recovery. These results support current guidelines to start HAART at a threshold of 350 cells/μl.