Mother-to-child transmission of HIV constitutes a substantial burden of new HIV infections in sub-Saharan Africa, and losses to follow-up continue to undermine prevention of mother-to-child transmission of HIV (PMTCT) programmes. This qualitative study sought to clarify why some women who were enrolled in a PMTCT programme in Lilongwe, Malawi, did not fully participate in follow-up visits in the first six months after testing HIV-positive. Twenty-eight women, 14 who participated fully in the programme and 14 who dropped out, were purposively selected for in-depth interview at two clinics. Focus group discussions with 15 previously interviewed and 13 newly recruited women were also conducted. Discussions with 12 of the women's husbands were also carried out. Although the proportion of women being tested has reportedly increased, losses to follow-up have shifted and are occurring at every step after testing. Major emerging themes associated with dropping out of the PMTCT programme within six months after delivery were to avoid involuntary HIV disclosure and negative community reactions, unequal gender relations, difficulties accessing care and treatment, and lack of support from husbands. The whole approach to the delivery of the PMTCT programme and home visits must be reconsidered, to improve confidentiality and minimise stigmatization. Women need to be empowered economically and supported to access HIV treatment and care with their partners, to benefit their whole family.