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The rate of comorbidities not related to human immunodeficiency virus (HIV) infection or acquired immunodeficiency syndrome (AIDS) among HIV-infected patients may be higher than expected. We assessed the incidence of comorbidities not related to HIV infection or AIDS by CD4 cell count and highly active antiretroviral therapy (HAART) use status in an HIV clinical practice. A total of 2824 patients contributed 9172 person-years of longitudinal data during the period 1997-2006. Among patients with a CD4 cell count <350 cells/mm3, receipt of HAART was associated with a significantly decreased incidence of comorbidities not related to HIV infection or AIDS.