Background: Fat distribution, bone mineral density (BMD) and mitochondrial DNA (mtDNA) may improve, in the long-term, after switching from nucleoside reverse transcriptase inhibitors (NRTIs) to fixed-dose abacavir (ABC)/ lamivudine (3TC) or tenofovir (TDF)/emtricitabine (FTC). Methods: This was a prospective, randomized, open-label, multicentre substudy of the BICOMBO trial in which virologically suppressed patients had their NRTIs switched to ABC/3TC or TDF/FTC. Whole-body dualenergy X-ray absorptiometry (DXA) was used to measure limb, trunk and total body fat and total BMD. Lumbar and hip DXA scans were used to measure lumbar and hip BMD. Fat mass ratio (FMR; % trunk fat/% leg fat by whole-body DXA) was used to assess fat distribution. mtDNA was measured in peripheral blood mononuclear cells (PBMCs). Parameters of interest were measured at baseline, 48 and 96 weeks, and were compared between treatment groups. Results: Of 56 patients included, 45 (20 ABC/3TC and 25 TDF/FTC) completed the substudy. After 96 weeks, ABC/3TC (+756 g, +12.1%) and TDF/FTC (+337 g, +7.6%) led to non-significantly different increases in limb fat (P=0.60). By contrast, trunk fat showed a significant increase (P=0.04) with ABC/3TC (+1,184 g, +10.6%) relative to TDF/FTC (-370 g, -4.2%). Median (IQR) FMR remained unchanged with ABC/3TC (-0.01 [-0.16-0.06]; P=0.23), but it decreased significantly with TDF/FTC (-0.13 [-0.30-0.00]; P=0.007). Total BMD and mtDNA significantly increased after 96 weeks, without differences between groups. Conclusions: Switching from NRTIs to either ABC/3TC or TDF/FTC led to similar increases in limb fat, BMD and PBMC mtDNA after 96 weeks. ©2012 International Medical Press.