The prevalence and the factors involved in discordant responses to highly active antiretroviral therapy were analysed in a closely followed cohort of 51 naïve HIV-infected patients at 48 weeks. A complete treatment response was considered as an increase in CD4 cell count of >or=50 cells/mm3 with a >or=1 log10 decrease in viral load or viral suppression. Virologic response (<50 CD4+ cells/mm3 increase) and immune response (<1 log10 decrease in viral load) were observed in 15.7% and 5.8% of the patients, respectively. We demonstrated that the prevalence of virologic response decreased at week 72 and disappeared after 96 weeks of treatment. This slower response did not correlate with protease inhibitor-based (PI-based) regimens or HCV coinfection. On the other hand, immune response in our cohort could be easily attributable to a simple mechanism, i.e. irregular treatment compliance.