Cardiac autonomic dysfunction has been examined in myasthenia gravis but not in congenital myasthenic syndromes (CMS). We aimed to evaluate cardiac autonomic functions in genetically defined CMS. Patients diagnosed with and under treatment for CMS were reviewed for 24-hour cardiac rhythm monitoring. Heart rate variability (HRV) measures were defined as: SDNN, mean of the standard deviations for all R-R intervals; SDNNi, standard deviation of all R-R intervals in successive five-minute epochs; RMSSD, square root of the mean of squared differences between successive R-R intervals. Ten patients with mutations in the epsilon subunit of the acetylcholine receptor (AChRepsilon) and five patients with mutations in the collagen-like tail of asymmetric acetylcholinesterase (ColQ) were included. Median age at evaluation was 17 (2.5-46) years. In the AChRepsilon group, RMSSD values; and in the ColQ group, SDNN, SDNNi and RMSSD values were significantly lower than those of healthy subjects. This first extensive report examining HRV in CMS showed alterations in patients with ColQ mutations and, to a lesser extent, in the group with AChRepsilon mutations. This might indicate an increased risk of cardiac arrhythmias. We suggest cardiological follow-up in CMS, and consideration of any potential cardiovascular effects of therapeutic agents used in management.