Efavirenz (EFV) causes neuropsychiatric side-effects and an unfavorable blood lipid profile. We investigated the effect of replacing EFV with raltegravir (RAL) on patient preference, daytime sleepiness, sleep quality, anxiety, and lipid levels.Switch-ER was a randomized, double-blind, cross-over study. Patients who tolerated EFV, with less than 50 copies/ml HIV-RNA, were randomized into two groups: the RAL-first group started with RAL (400 mg twice daily) and EFV placebo, and the EFV-first group with EFV (600 mg once daily) and RAL placebo. After 2 weeks, both groups switched to the alternate regimen. The primary endpoint was patient preference for the first or the second regimen, assessed after 4 weeks.Fifty seven participants were enrolled with a median CD4 cell count 600/μl, and duration of previous EFV therapy 3.4 years. Fifty three participants completed the study. When asked about treatment preference after 4 weeks, 22 preferred RAL and 12 preferred EFV, whereas 19 did not express a preference. A significant difference in anxiety and stress scores favoring RAL (P = 0.04 and 0.03, respectively) was observed. Median plasma cholesterol levels decreased by 0.4 mmol/l (16 mg/dl, P < 0.001), triglycerides by 0.2 mmol/l (18 mg/dl, P = 0.036), and low-density lipoprotein by 0.2 mmol/l (8 mg/dl, P = 0.004) after replacing EFV with RAL. After study completion, 51% of patients switched to RAL.Half of patients previously on a stable EFV preferred to switch to RAL, after double-blind exposure to RAL for 2 weeks. Substitution of EFV by RAL significantly impacted on lipid levels, stress, and anxiety scores.