Although a scientific and ethical debate about the possible reproductive options for carriers of mitochondrial DNA (mtDNA) mutations is developing, not much information regarding the views and experiences of professionals exists. This paper explores the attitudes and experiences of professionals involved on a daily basis with their patients' reproductive decision-making in the context of mtDNA disease. Qualitative international multicenter design using in-depth semi-structured interviews with 20 professionals has been utilized. We identified four main themes emerging from the interviews. Firstly, we illustrate the discussion among professionals as to what extent mitochondrial genetics differs from other areas in genetics, both technically and ethically. Secondly, we show the discomfort and doubts of professionals when an mtDNA mutation is involved, because of the uncertainty remaining after testing. Thirdly, we discuss how professionals struggle with the tension between, on the one hand, the ideal of reproductive autonomy and, on the other hand, the reality of their professional responsibility and complex clinical decision-making. Fourthly, we delineate the strategies used by professionals in order to make attempts to control uncertainty. This paper illustrates the impact on professionals of reproductive decision-making in the context of mtDNA disease. It shows their feelings of discomfort when interpreting and explaining uncertain or ambiguous data and may be perceived as an example of how professionals deal with the inherent limitations in genetic knowledge representing the state of the art. Insight into the experiences of professionals may contribute to a further improvement of reproductive genetic counseling in the context of mtDNA disorders.