BackgroundIt is well documented that mothers of children with intellectual disabilities or autism experience elevated stress, with mental health compromised. However, comparatively little is known about mothers of children with rare genetic syndromes. This study describes mental health and well-being in mothers of children with 13 rare genetic syndromes and contrasts the results with mothers of children with autism.MethodsMothers of children with 13 genetic syndromes (n = 646; Angelman, Cornelia de Lange, Down, Fragile-X, Phelan McDermid, Prader-Willi, Rett, Rubenstein Taybi, Smith Magenis, Soto, Tuberous Sclerosis Complex, 1p36 deletion and 8p23 deletion syndromes) and mothers of children with autism (n = 66) completed measures of positive mental health, stress and depression. Using Bayesian methodology, the influence of syndrome, child ability, and mother and child age were explored in relation to each outcome. Bayesian Model Averaging was used to explore maternal depression, positive gain and positive affect, and maternal stress was tested using an ordinal probit regression model.ResultsDifferent child and mother factors influenced different aspects of mental well-being, and critically, the importance of these factors differed between syndromes. Maternal depression was influenced by child ability in only four syndromes, with the other syndromes reporting elevated or lower levels of maternal depression regardless of child factors. Maternal stress showed a more complex pattern of interaction with child ability, and for some groups, child age. Within positive mental health, mother and child age were more influential than child ability. Some syndromes reported comparable levels of depression (SMS, 1p36, CdLS) and stress (SMS, AS) to mothers of children with autism.ConclusionsBayesian methodology was used in a novel manner to explore factors that explain variability in mental health amongst mothers of children with rare genetic disorders. Significant proportions of mothers of children with specific genetic syndromes experienced levels of depression and stress similar to those reported by mothers of children with autism. Identifying such high-risk mothers allows for potential early intervention and the implementation of support structures.Electronic supplementary materialThe online version of this article (10.1186/s13023-018-0924-1) contains supplementary material, which is available to authorized users.