Abstract Background Parents of individuals with rare neurodevelopmental conditions and intellectual disabilities (ID) are vulnerable to mental health difficulties, which vary between parents and within parents over time. The underlying cause of a child’s condition can influence parents’ mental health, via uncertain pathways and within unknown time-windows. Results We analysed baseline data from the IMAGINE-ID cohort, comprising 2655 parents of children and young people with ID of known genetic origin. First, we conducted a factor analysis of the SDQ Impact scale to isolate specific pathways from genetic aetiology to parents’ mental health. This suggested a two-factor structure for the SDQ Impact scale, with a “home & distress” dimension and a “participation” dimension. Second, we tested via structural equation modelling (SEM) whether genetic diagnosis affects Impact and mental health directly, or indirectly via children’s characteristics. This analysis identified an indirect pathway linking genetic aetiology to parents’ mental health, serially through child characteristics (physical disabilities, emotional and behavioural difficulties) and Impact: home & distress. Third, we conducted moderation analysis to explore the influence of time elapsed since genetic diagnosis. This showed that the serial mediation model was moderated by time since diagnosis, with strongest mediating effects among recently diagnosed cases. Conclusions There are multiple steps on the pathway from ID-associated genetic diagnoses to parents’ mental health. Pathway links are strongest within 5 years of receiving a genetic diagnosis, highlighting opportunities for better post-diagnostic support. Recognition and enhanced support for children’s physical and behavioural needs might reduce impact on family life, ameliorating parents’ vulnerabilities to mental health difficulties.