Objectives. To identify the barriers that limit compliance with the prevention of mother-to-child transmission (PMTCT) of HIV measures in two indigenous communities of the Amazon region of Peru. Materials and methods. Qualitative study with a phenomenological approach. Semi-structured interviews were conducted with pregnant women and mothers of children younger than 1 year of the awajún and wampis indigenous communities diagnosed with HIV in the period 2014–2015. Results. The study sample included 15 of 29 eligible women and 87% were Awajún. Limitations and possible negative effects were observed in cases in which sanitary measures for PMTCT were imposed. Considering their knowledge of diseases, including the presence of symptoms and disabilities, many women from these communities do not believe they are infected with HIV and consider the diagnosis a lie or relate the diagnosis to harm, and these beliefs limit their compliance with medical indications and decrease their trust in health services. In addition, the women believe that their children will inevitably be born sick and will die soon, and thus consider cesarean sections and child care a futile effort. Other factors influencing the successful implementation of PMTCT measures include language barriers, remoteness of health centers, and the fear of judgment and moral condemnation by the local community. Conclusions. PMTCT measures challenge the customs, values, and beliefs of pregnant women and mothers in the Awajún and Wampis indigenous communities, and thus these measures are not understood or accepted, jeopardizing the relationship of the mothers with health personnel. Therefore, cultural factors and interventions appropriate to this population must be better understood.