BACKGROUND: To examine the relationships of rare genetic diseases affecting skeletal development, socio-demographic characteristics, and oral health-related behaviours with dental clinical measures in children and adolescents. METHODS: A cross-sectional study paired by age, gender and social class included 61 children and adolescents with osteogenesis imperfecta (n = 40) or mucopolysaccharidoses (n = 21) and those without genetic rare diseases (n = 60). Participants were selected at two referral hospitals for rare genetic diseases in the city of Belo Horizonte, Brazil. Caregivers completed a questionnaire to obtain age, gender, caregiver's schooling, social class, patterns of dental attendance and duration of breastfeeding. Oral hygiene, dental caries, dental anomalies and malocclusion were assessed through dental examinations. The relationships between variables were estimated through Pathway analysis using the maximum likelihood method. RESULTS: Rare genetic diseases affecting skeletal development were directly associated with dental caries (β = 0.22), dental anomalies (β = 0.36) and malocclusion (β = 0.29). They were also inversely linked to a preventive pattern of dental attendance (β = -0.25). Rare genetic diseases affecting skeletal development were associated with poor oral hygiene (β = 0.28) and shorter breastfeeding duration (β = -0.21). Rare genetic diseases affecting skeletal development were linked indirectly with dental caries, a reduced pattern of dental attendance and poor oral hygiene (β = 0.43). Patterns of dental attendance mediated the link between rare genetic diseases affecting skeletal development and malocclusion (β = -0.05). CONCLUSION: Rare genetic diseases affecting skeletal development were associated with poor oral health. Patterns of dental attendance and poor oral hygiene mediated the link between rare genetic diseases affecting skeletal development and dental clinical measures.