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Background: In clinical trials, highly active antiretroviral therapy (HAART) reduces plasma HIV-1 RNA levels to less than 500 copies/mL in 60% to 90% of patients with HIV-1 infection. The performance of such therapy outside of the clinical trial setting is unclear.Objective: To determine factors associated with failure to suppress HIV-1 RNA levels and adverse drug reactions in a cohort of patients in whom protease inhibitor-containing therapy was begun in a large urban clinic.Design: Retrospective cohort study.Setting: Johns Hopkins HIV Clinic in Baltimore, Maryland.Patients: 273 protease inhibitor-naive patients began taking a protease inhibitor regimen containing at least one other antiretroviral drug to which the patients had not previously been exposed.Measurements: Demographic variables, plasma HIV-1 RNA levels, CD4+ lymphocyte counts, and adverse drug reactions.Results: Levels of HIV-1 RNA were undetectable in 42% of the cohort at 1 to 90 days, in 44% at 3 to 7 months, and in 37% at 7 to 14 months. Factors associated with failure to suppress viral load at two or more time points included higher rates of missed clinic appointments, nonwhite ethnicity, age 40 years or younger, injection drug use, lower baseline CD4+ lymphocyte count, and higher baseline viral load. In a multivariate model, only higher rates of missed clinic appointments were independently associated with viral suppression at 1 year. Ritonavir was associated with adverse drug reactions about twice as frequently as indinavir or nelfinavir, and women experienced significantly more adverse effects than men.Conclusions: Unselected patients in whom HAART is started in a clinic setting achieve viral suppression substantially less frequently than do patients in controlled clinical trials. Missed clinic visits were the most important risk factor for failure to suppress HIV-1 RNA levels. Studies are needed to identify interventions that maximize the performance of HAART in inner-city clinics. [ABSTRACT FROM AUTHOR]