While HAART allows for the reconstitution of immune functions in most treated HIV patients, discrepant responses including failure to achieve a significant increase in circulating CD4+ T cells despite undetectable plasma viral loads (pVL), or a good immunological response while not reaching undetectable viremia, may occur. Thus, to evaluate the incidence of and risk factors for discrepant responses to HAART, we conducted a retrospective study of all 446 patients treated with HAART between 1 January 1998 and 31 August 2004 in our HIV unit. CD4+ T cell counts and pVL values at baseline and end of study were parameters of the type of response. Within a mean follow-up period of 33 months, discrepant immunological and virological responses occurred in even 50% patients. Of these, 174 (39%) did not have a rise in CD4+ T cells to above 400 per μl despite a good virological response (type 1 dissociation), while 49 (11.0%) had a rise in the CD4+ T cell count to at least 200 per μl but their pVL was not undetectable (type 2 dissociation). The risk factors for immunological failure despite an undetectable pVL were baseline CD4+ T cells below 100 per μl (OR 1.44, 95%CI 1.02–2.03) and HAART composed of three NRTIs (OR 1.92, 95%CI 1.35–2.73), while usage of two NRTIs in combination with PI(s) (OR 0.36, 95%CI 0.26–0.49), as well as simultaneous usage of all three drug classes (OR 0.37, 95%CI 0.26–0.53) were shown to be protective. The usage of PI-containing HAART regimens was protective against type 2 dissociation (OR=0.40, 95%CI 0.19–0.83). Importantly, there were no differences in the survival of HAART-treated patients irrespective of the type of response.