OBJECTIVE: To assess the association of sleep disorders with the findings of heart rate variability (HRV) in children and adolescents with cystic fibrosis (CF). METHODS: Cross-sectional study including children and adolescents aged six to 18 years with a clinical diagnosis of CF. Sociodemographic and clinical data were collected. Sleep disorders were evaluated using baseline nocturnal polysomnography. The autonomic nervous system (ANS) was evaluated through resting HRV. RESULTS: A total of 30 individuals (11.2 years) with a mean forced expiratory volume in the first second (FEV1) of 62.7% were included. The respiratory disturbance index presented a median of 2.6 and obstructive sleep apnea syndrome (OSAS) was identified in 30%. In the HRV analysis, a mean standard deviation of all inter-beat (RR) intervals (SDNN) of 60.8+/-45.9ms was found. There was a significant correlation between the HRV low-frequency/high-frequency (LF/HF) global modulation index and the minimum SpO2 during sleep in patients with FEV1<60% (r=0.71; p=0.02). The prevalence of sleep disorders and HRV abnormalities was higher in individuals with lesser pulmonary function (FEV1<60%). CONCLUSIONS: The results indicate a weak correlation of sleep disorders (minimum SpO2) with HRV parameters (LH/HF) in children and adolescents with CF. When pulmonary function was reduced, a stronger correlation was found, highlighting the influence of disease severity. A high prevalence of ANS disorders, nocturnal hypoxemia, and presence of OSAS was also found.