BACKGROUND: Cystic fibrosis (CF) is a multisystem disease that affects the cardiorespiratory system and the cardiac autonomic control may be altered at rest and after a submaximal exercise. OBJECTIVE: To assess the cardiac autonomic control by heart rate variability (HRV) analysis before and after a 6-minute walk test (6MWT). METHOD: Thirteen children diagnosed with Cystic Fibrosis (CFG) aged 12+/-2.7 years (FEV1/FVC: 0.83+/-0.11, FEV1: 71.4+/-21 %pred) and 12 healthy children (control group-CG) aged 11.4+/-2.4 years (FEV1/FVC: 0.91+/-0.12, FEV1: 91.6+/-17.4 %pred) were included in the study. HRV was evaluated prior to and immediately after the 6MWT and the heart rate recovery assessed on the first and second minute after test. RESULTS: Prior to exercise, CF patients presented higher values for the variables LF(nu) (53.2+/-15.0 vs. 32.8+/-7.9, p=0.0003) and LF/HF (1.25+/-0.72 vs. 0.49+/-0.18, p<0.006) as well as lower values of HF(%) (25.4+/-18.4 vs. 53+/-9.6, p=0.002) and HF(nu) (47.3+/-14.7 vs. 68.3+/-8.7, p0.001) when compared to CG. After the 6MWT, both groups demonstrated HRV recovery to baseline levels; however, the differences between CFG and CG were maintained for the variables LF(ms 2) (846.7+/-754.8 vs. 345.6+/-197.2, p=0.02); LF(%) (35.4+/-8.1 vs. 25.9+/-6.2, p=0.002); LF(nu) (60.0+/-16.3 vs. 34.9+/-8.7, p<0.0001); HF(%) (27.4+/-13.7 vs. 48.1+/-6.3, p=0.0003); HF(nu) (40.4+/-15.8 vs. 65.6+/-8.2, p=0.0003) and LF/HF (1.9+/-1.7 vs. 0.5+/-0.2, p=0.0001). CONCLUSIONS: Children with cystic fibrosis exhibited predominance of sympathetic activity at rest that persisted after the 6-minute walking test when compared to the control group.