Prior to 2011, uptake of PMTCT in Malawi remained low despite increased access to antiretrovirals. We sought to understand barriers to PMTCT in rural Malawi. Twenty-two HIV-infected pregnant and postpartum women in PMTCT programs were interviewed in Nkhoma, Malawi, between April-May 2010. All women were staged by WHO criteria or CD4 count as ineligible for three-drug treatment by Malawi's HIV Guidelines at the time. The median age was 26 years (range 22-39) and 77% were married. Barriers to accessing PMTCT care included transportation to clinic, stigma in the community leading to avoidance of HIV disclosure, food insecurity, and providers' attitudes towards HIV-infected pregnant women. Given Malawi's transition to Option B+ for PMTCT in which women are initiated on antiretroviral therapy (ART) during pregnancy and continued for life, strategies to improve access and retention will need to address barriers and incorporate facilitators that motivate and retain women in HIV care.