Multimorbidity, defined as having two or more chronic health conditions, is associated with elevated polypharmacy and mortality. Autism spectrum disorder is a whole-body chronic health condition in which comorbidities – in particular co-occurring intellectual disability – contribute to high clinical heterogeneity, polypharmacy and premature mortality. We aimed to determine specific multimorbidity patterns among autism spectrum disorder + intellectual disability adults, and to identify participants’ subgroups based on multimorbidity features. We used baseline examination data from a previous exploratory prospective multicentric study that included 63 autism spectrum disorder + intellectual disability adults. Multimorbidity patterns and subgroups were determined using clustering approaches. We observed 84.1% multimorbidity, significantly associated with age. We identified a dominant multimorbidity pattern, combining immune dysfunction, gastrointestinal disorders, neurological, and joint diseases. Four participants’ subgroups could be distinguished by multimorbidity, autonomy and polypharmacy. Two clusters were distinguished by the prevalence and consequences of multimorbidity. One cluster involved women with endocrine disorders. The final cluster was composed of older adults with the lowest autism spectrum disorder severity but greater multimorbidity, including cardiovascular and kidney diseases. Our results support a role for the gut–brain axis in the pathophysiology of autism spectrum disorder + intellectual disability multimorbidity. Furthermore, we identified patient subgroups with specific needs, underscoring the importance of a holistic approach for autism spectrum disorder + intellectual disability adults. Lay abstract: Multimorbidity relates to having multiple chronic health conditions. It is a risk factor for poor health and reduces life expectancy. Autistic people have multiple chronic health conditions and die prematurely, especially if they have an intellectual disability (autism spectrum disorder and intellectual disability). Certain pathophysiological processes observed in autism spectrum disorder are common to those related to the genesis and/or maintenance of multimorbidity. Furthermore, multimorbidity could be helpful in better identifying patient subgroups in autism spectrum disorder. It is therefore essential to better characterize multimorbidity and its consequences in the subgroup of autism spectrum disorder + intellectual disability individuals to offer them personalized care. We conducted a preliminary study of 63 autism spectrum disorder + intellectual disability adults to classify them according to their multimorbidity and search for a specific combination of chronic health conditions. We observed high and early multimorbidity in this sample and identified four classes of participants, distinguished by their multimorbidity status, independence and number of treatments. In addition, we observed a dominant combination of multimorbidity in our sample, combining immune dysfunction and gastrointestinal disorders, neurological and joint diseases. These findings support the hypothesis that an altered gut–brain relationship is involved in the risk of autism spectrum disorder, its outcome, and its association with chronic health conditions. Although larger studies are needed, our results suggest that subgroups of autism spectrum disorder + intellectual disability individuals can be identified based on their multimorbidity and potentially different ageing trajectories. A more comprehensive and personalized approach is needed to reduce the burden of multimorbidity and increase the quality of life and life expectancy in autism spectrum disorder/ intellectual disability.