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Abstract Background To date, no studies have investigated the prevalence of post-COVID-19 conditions in patients with Intellectual and Developmental Disabilities (IDD). Addressing this research gap is crucial, as understanding post-COVID-19 conditions in IDD patients can improve care planning, and it is essential not to overlook this vulnerable population in COVID-19 studies. This study was aimed at investigating the prevalence of post-COVID-19 conditions in patients with IDD and compare their risk with that of the general population. Methods Using the TriNetX network, we identified patients with and without an IDD who had COVID-19. Subsequently, we compared the risk of developing any post-COVID-19 condition between these two groups, during the 90–180-day follow-up after SARS-CoV-2 infection. Results During the follow-up, patients with an IDD exhibited a significantly higher prevalence of post-COVID-19 conditions compared to the general population (hazard ratio [HR], 1.120; 95% confidence interval [CI]: 1.053–1.191). Specifically, COVID-19 survivors with IDD had a significantly increased risk of experiencing abnormal breathing (HR, 1.216; 95% CI: 1.077–1.373), abdominal symptoms (HR, 1.259; 95% CI: 1.128–1.406), fatigue (HR, 1.397; 95% CI: 1.216–1.606), anxiety/depression (HR, 1.157; 95% CI: 1.050–1.274), cognitive symptoms (HR, 1.828; 95% CI: 1.529–2.186), myalgia (HR, 1.325; 95% CI: 1.077–1.631), sleep disturbances (HR, 1.481; 95% CI: 1.148–1.910), and cough (HR, 1.315; 95% CI: 1.146–1.508) compared to the non-IDD group. Conclusions Patients with IDD might be associated with a higher risk of post-COVID-19 conditions following SARS-CoV-2 infection compared to the general population.