Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disease with low prevalence in pediatrics. Health studies have not sufficiently analyzed the role of psychological variables in rare diseases such as PCD. This paper studies the psychological characteristics of a group of pediatric patients diagnosed with PCD compared to their healthy peers. The sample consisted of 48 preadolescents-adolescents, aged 9-18 years (M = 12.96; SD = 2.71), with similar distribution by sex, and 25% of the patients having dyskinesia. Clinical anxiety-depression, self-esteem and psychological well-being were evaluated using questionnaires: the Adolescent Psychological Well-being Scale (BIEPS-J), the Hospital Anxiety and Depression Scale (HADS) and the Rosenberg Self-Esteem Scale (RSE). Data were analysed using descriptive, mean comparison (t-test) and diffuse comparative qualitative analysis (QCA). The results show no differences were found between healthy and PCD patients in the variables analyzed, except for social ties showing the latter greater well-being in this aspect. In QCA models, the variables that best explained the high or low levels of well-being were depression and selfesteem, and primary ciliary dyskinesia was not a necessary condition for presenting low levels of well-being. In conclusion, our results highlight the need to explore psychological aspects in pediatric patients with rare diseases.