Background Determining the actiology of intellectual disability (ID) enables anticipation of specific comorbidity and can thus be beneficial. Blood sampling, however, is considered stressful for people with ID. Our aim was to evaluate the feasibility of a non-invasive screening technique of nine microdeletions/duplications among adults with ID of unknown aetiology. Methods In a random sample Of 300 adult clients of Dutch ID services without an aetiological diagnosis, DNA was collected on site using oral swabs. Multiplex Ligation-dependent Probe Amplification was applied to screen for nine microdeletions/ duplications related to ID syndromes (Williams 22q11-deletion, 1p-deletion, Miller-Dieker, Smith-Magenis, Prader-Willi, Alagille, Saethre-Chotzen and Sotos syndrome). Results Feasibility: prior to the consent procedure, for 2.1% (10/471 eligible participants), the method was considered undesirable. In 0.7% (2/300 participants) oral swabs failed because of resistant behaviour, while in 16.1% (48/298 swabs) analysis was unsuccessful because of insufficient amounts of DNA. A repeated attempt yielded an equal success rate. Outcome Microdeletions were diagnosed in four participants: 22q11 deletion (n = 2), 5q35 deletion (Sotos syndrome) (n = 1) and 1p deletion (n = 1). One participant had a duplication of the Prader Willi Region (15q11-13) owing to mosaicism of a supernumerary marker chromosome (15). Conclusions Oral swabs are a feasible method for DNA sampling in adults with IDs. A diagnosis could be made in five Out Of 275 people with ID of unknown aetiology. After screening, in the total population sample (n = 620), the prevalence of syndromes associated with the microdeletions/ duplications studied was at least 2.3% (95% confidence interval 1.1-3.4%).