Nineteen patients who completed a 27-month CD4-guided structured treatment interruption (STI) trial that showed similar efficacy in STI and continuous arms were asked to choose CD4-guided versus continuous HAART after the study ended. Six chose STI and 13 chose continuous HAART. Reasons for not choosing STIs were fear of developing HIV-related illnesses (38%), fear of CD4 drop (30.8%), fear of viral load increase (7.7%) and ease (7.7%). Those who preferred CD4-guided HAART had a higher median CD4 count nadir during STI and fewer on-off cycles. This study provides an important insight into the preference of patients towards STI in a resource-limited setting.