Abstract Background Chronic disease and comorbidity patterns in people with intellectual disabilities (ID) are more complex than in the general population. However, incomplete understanding of these differences limits care providers in addressing them. Objective To compare chronic disease and comorbidity patterns in chronically ill patients with and without ID in Dutch general practice. Methods In this population-based study, a multi-regional primary care database of 2018 was combined with national population data to improve identification of adults with ID. Prevalence was calculated using Poisson regression to estimate prevalence ratios and 95% confidence intervals for the highest-impact chronic diseases (ischemic heart disease (IHD), cerebrovascular disease (CVD), diabetes mellitus (DM), and chronic obstructive pulmonary disease (COPD)) and comorbidities. Results Information from 18,114 people with ID and 1,093,995 people without ID was available. When considering age and sex, CVD (PR = 1.1), DM (PR = 1.6), and COPD (PR = 1.5) times more prevalent in people with than without ID. At younger age, people with ID more often had a chronic disease and multiple comorbidities. Males with ID most often had a chronic disease and multiple comorbidities. Comorbidities of circulatory nature were most common. Conclusions This study identified a younger onset of chronic illness and a higher prevalence of multiple comorbidities among people with ID in general practice than those without ID. This underlines the complexity of people with ID and chronic diseases in general practice. As this study confirmed the earlier onset of chronic diseases and comorbidities, it is recommended to acknowledge these age differences when following chronic disease guidelines.