ObjectivesTo investigate the challenges of, and opportunities for, effective delivery of prevention of mother-to-child transmission (PMTCT) services from the perspectives of primary healthcare providers in Lagos, Nigeria.DesignThis qualitative study consisted of nine focus groups with 59 health providers, analysed thematically.SettingThirty-eight primary health facilities in central and western districts of Lagos, Nigeria.ParticipantsParticipants included nurses, nursing assistants, community health workers, laboratory workers, pharmacists, pharmacy technicians, monitoring and evaluation staff and medical records personnel.ResultsHealth providers’ challenges included frustration with the healthcare system where unmet training needs, lack of basic amenities for effective and safe treatment practices, low wages and inefficient workflow were discussed. Providers discussed patient-level challenges, which included the practice of giving fake contact information for fear of HIV-related stigmatisation, and refusal to accept HIV-positive results and to enrol in care. Providers’ suggestions for addressing PMTCT service delivery challenges included the provision of adequate supplies and training of healthcare workers. To mitigate stigmatisation, participants suggested home-based care, working with traditional birth attendants and religious institutions and designating a HIV health educator for each neighbourhood.ConclusionsFindings illustrate the complex nature of PMTCT service delivery and illuminate issues at the patient and health system levels. These results may be used to inform strategies for addressing identified barriers and to improve the provision of PMTCT services, thus ensuring better outcomes for women and families.