The Pediatric Sleep Questionnaire described by Chervin et al. (Sleep Medicine, 2000, 1, 21–32) was originally validated for children with obstructive sleep apnoea syndrome but without other disorders. The aim of our study was to check the applicability of this questionnaire in children with underlying chronic medical conditions. Children aged 2–18 years who underwent a diagnostic sleep study at Great Ormond Street Hospital were recruited over a 10-month period. The Pediatric Sleep Questionnaire completed by their parents and cardiorespiratory polygraphy were scored. Sensitivities and specificities of the Pediatric Sleep Questionnaire were calculated using a Pediatric Sleep Questionnaire score of 0.33 as being indicative of sleep-disordered breathing. A total of 561 patients were reviewed. Neuromuscular disorders (n = 108), craniofacial anomalies (n = 58) and the obstructive sleep apnea syndrome control group (n = 155) were best represented. The sensitivity for patients with isolated obstructive sleep apnoea syndrome was 76.5% when using an apnoea–hypopnoea index ≥ 5, but this was much lower when looking at specific sub-groups such as neuromuscular patients (25%) or patients with Trisomy 21 (36.7%). Sensitivities remained unchanged for patients with obstructive sleep apnoea syndrome (77.3%) when an apnoea–hypopnoea index of ≥ 1 was used, but improved for neuromuscular disorders sub-groups (36.7%) and Trisomy 21 (84%). In conclusion, the Pediatric Sleep Questionnaire is not a good screening tool for obstructive sleep apnoea syndrome in children with complex underlying disorders when a cut-off apnoea–hypopnoea index of ≥ 5 is used, and it cannot replace cardiorespiratory polygraphy recording.