UNAIDS has set a goal of achieving the elimination of mother-to-child transmission (eMTCT) of HIV by 2015 and keeping HIV-positive (HIV+) mothers alive. In pursuit of this goal, in 2011, the Malawi Ministry of Health (MoH) adopted the Option B+ strategy, which entails lifelong antiretroviral treatment for all HIV+ mothers, irrespective of severity of HIV infection. Poor mother-child pair retention is one of the major challenges against achieving this goal. To improve retention of mother-infant pairs in the eMTCT continuum of care, the Promoting Retention among Infants and Mothers Effectively (PRIME) study is evaluating the effectiveness of 3 models of health care delivery namely, mother-infant pair clinics, which deliver integrated HIV and non-HIV services, mother-infant pair clinics plus electronic text message (SMS) reminders for mother-infant pairs who miss scheduled eMTCT follow-up clinics, and current standard of care. The primary outcome is "the proportion of HIV+ mothers and/or HIV-exposed infants (HEI) retained in eMTCT care at 12 months postpartum and received recommended HIV and non-HIV services during preceding scheduled visits." This 3-arm cluster randomized intervention study is being implemented in 30 primary health facilities (10 facilities per arm) in Mangochi and Salima districts, Malawi. At each clinic, a total of 41 HIV+ mothers attending maternal and child health services are being recruited and followed up for 18 months postpartum. This article describes the study methodology and interventions, successes and challenges experienced during the first 12 months of study implementation and relevance of study results to Malawi and other countries adopting the Option B+ strategy.