BackgroundPrimary carnitine deficiency is an inborn error of metabolism, which can lead to life-threating complications early in life. Low carnitine levels can be detected by newborn bloodspot screening (NBS). However, NBS can also identify, mostly asymptomatic, mothers with primary carnitine deficiency. To identify mothers’ needs and areas for improving screening practice, this study explored the experiences with, and opinions on primary carnitine deficiency screening in NBS among women diagnosed through NBS of their newborn.MethodsTwelve Dutch women were interviewed, 3–11 years after diagnosis. Data were analysed using a thematic approach.ResultsFour main themes were derived: 1) psychological impact of primary carnitine deficiency diagnosis, 2) becoming a patient and “patient-in-waiting”, 3) information issues and care provision, and 4) primary carnitine deficiency as part of the NBS panel. Mothers shared that they did not experience major psychological distress of the diagnosis. They did experience (recall) various emotions following the initial abnormal NBS result, including fear and anxiety as well as relief, and emotions regarding their own diagnosis, including uncertainty about health risks and treatment effectiveness. Some felt a patient-in-waiting. Many participants experienced a lack of information, especially shortly after receiving the abnormal NBS result. All shared the belief that screening for primary carnitine deficiency in NBS is beneficial for the newborn, and, given the information they received, also considered the knowledge beneficial for their own health.ConclusionsPsychological burden following diagnosis was experienced by women as limited, although the experienced lack of information amplified feelings of uncertainty and anxiety. Most mothers believed that benefits of knowing about primary carnitine deficiency outweighed the disadvantages. Mothers’ perspectives should be incorporated in policy-making about primary carnitine deficiency in NBS.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13023-023-02735-0.