Risk of developing drug resistance after stopping antiretroviral regimens to prevent mother-to-child HIV-1 transmission (PMTCT) is unknown. Mma Bana Study randomized treatment-naïve pregnant women with CD4 ≥200 cells/mm3 to receive either abacavir/zidovudine/lamivudine (triple NRTI arm) or lopinavir/ritonavir/zidovudine/lamivudine (PI arm). Drugs were discontinued after 6 months breastfeeding. One month post-discontinuation, 29 NRTI arm samples and 25 PI arm samples were successfully genotyped. No clinically significant antiretroviral resistance mutations were detected. Eight minor resistance mutations were found among 11(20%) women (3 from NRTI arm, 8 from PI arm), occurring at similar frequencies to those reported in HIV-1 subtype C treatment naive cohorts.