Objectives: The aim of this study was to compare the prevalence of oral diseases (caries, periodontal disease, enamel defects) between patients with phenylketonuria (PKU), their siblings, and a matched control group. Materials and methods: A total of 109 patients with PKU, 14 siblings of PKU patients, and 100 healthy individuals aged 6 to 68 years were recruited. All participants completed a questionnaire based on their health status. The patients’ decayed/missing/filled teeth index (dmft/DMFT), gingival bleeding index (GBI), plaque control record (PCR), periodontal screening and recording index (PSR), and developmental enamel defects index (DDE) were recorded. Descriptive statistics and regression modeling were used to examine potential associations between the exposure and the outcomes of interest. Results: Patients with PKU had 1.6 times more caries (95% confidence interval (CI) 1.22 to 2.20; p = 0.001), seven times more enamel defects (95% CI 3.94 to 14.21; p < 0.001), and four times higher PSR values (95% CI 2.26 to 7.15; p < 0.001) than the control group. The siblings had significantly fewer enamel defects but no significant differences in caries and periodontal parameters compared to the PKU patients. Conclusions: The results showed a higher risk for the development of caries, periodontitis, and enamel defects in PKU patients. Clinical relevance: Implementation of preventive measures and regular dental care is necessary for patients with PKU.