ObjectivesEvidence for nocturnal oximetry interpretation in patients with abnormal neuromuscular function is limited. We aimed to compare children with neuromuscular disease (NMD) or Prader‐Willi syndrome (PWS) to otherwise healthy subjects with obstructive sleep‐disordered breathing (SDB) or without respiratory disorder (controls) regarding nocturnal oximetry parameters.MethodsWe analyzed recordings from children with: (a) NMD; (b) PWS; (c) snoring and adenotonsillar hypertrophy and/or obesity (SDB); and (d) controls. Outcomes included: (a) basal SpO2; (b) proportions of subjects with McGill oximetry score (MOS) >1 (clusters of desaturations); and (c) desaturation index (SpO2 drops ≥3%/h‐ODI3).ResultsData of 12 subjects with NMD (median age, 5.2 years; IQR, 2.7, 8.2), 14 children with PWS (5 years; 2.3, 6.9), 21 children with SDB (5.8 years; 4.6, 9.6), and 20 controls (6.2 years; 5.4, 11.2) were analyzed. Children with NMD, PWS, and SDB had lower basal SpO2 than controls (95.6% [94.5%, 96.9%], 96.2% [95.1%, 97.4%], 96.1% [95.8%, 97.5%] vs 97.8% [97.2%, 97.9%], respectively; (P < .01). NMD and PWS showed the greatest negative effect on basal SpO2 (P < .05). Children with SDB or PWS had a higher risk of MOS >1 than patients with NMD (OR, 25.9 [95% CI, 3.4‐200.4] and 9.5 [1.5‐62.6]). NMD, PWS, and SDB were similar regarding ODI3, which was elevated compared to ODI3 in controls (P < .05). Frequent desaturations predominated in NMD, while periods of sustained desaturation were noted in NMD and PWS.ConclusionPWS and NMD have a negative effect on basal SpO2, while clusters of desaturations are prevalent in patients with PWS or obstructive SDB.