ABSTRACTRationaleCongenital central hypoventilation syndrome (CCHS) is a rare disorder characterized by alveolar hypoventilation and variable autonomic nervous system (ANS) dysfunction (ANSD) due to mutations in PHOX2B, a gene crucial for ANS neural crest lineage differentiation.Objectives and MethodsOur prospective study aims were twofold: to (1) assess the relationships between the subjective Composite Autonomic Symptom Score (COMPASS)‐31 and objective indices of ANSD obtained from heart rate variability analyses, ambulatory blood pressure (BP) monitoring, and CO2 chemosensitivities and (2) describe the organ system ANSD, its relationship to PHOX2B genotype, and its consequences on quality of life (PedsQL) in children with CCHS.ResultsThirty‐two PHOX2B mutation‐confirmed subjects (median [range] age 9.2 years (4.4; 18.0), 15 girls) were enrolled. COMPASS‐31 was assessed in 32 matched (sex and age, range: 4.3; 18.9 years) healthy controls. As compared to healthy controls, children with CCHS had increased vasomotor (p = 0.001), secretomotor (p = 0.021), gastrointestinal (p = 0.002) and pupillomotor (p = 0.028) scores and decreased orthostatic intolerance scores (p = 0.050). There was no difference in overall COMPASS‐31 score between CCHS and controls (p = 0.083). However, in CCHS, overall COMPASS‐31 scores correlated with high frequencies (HF) normalized (cardiac parasympathetic modulation: R = −0.53; p = 0.002), low frequencies (LF)/HF ratio (R = 0.56; p< 0.001), and both systolic and diastolic nighttime BP dipping (R = 0.45, p = 0.012 and R = 0.40, p = 0.028, respectively). No significant relationships between COMPASS‐31 scores and chemosensitivity testing, PedsQL scores, or PHOX2B genotype were identified.ConclusionsCOMPASS‐31 identified some aspects of CCHS‐related ANSD, and scores correlate with objective ANS function measures, supporting the potential utility of COMPASS‐31 in CCHS.