Abstract Background Prolongation of the PR interval is a common finding among competitive athletes. However, further investigations should be performed when the PR interval is markedly prolonged. We report the case of a young male athlete with a late progressive congenital form of autoimmune-mediated atrioventricular block. Case presentation A 26-year-old male athlete was referred to our center because of a significant prolongation of the PR interval (PR=400 ms), firstly found at the age of 7 years in a preparticipation screening and then confirmed when he was 10 years old. He has been playing soccer for 6 hours/week without symptoms or limitations. His personal remote medical history was unremarkable, he did not have a family history of sudden cardiac death, channelopathies, or cardiomyopathies. Vital parameters and physical examination were normal. Blood test results were within the limits, with negative inflammation indexes and normal thyroid function. Ambulatory 12-lead ECG monitoring, including a training session to assess the chronotropic response to exercise, showed a 1st and 2nd type 1 AV block with narrow QRS without pauses and a shortening of the PR interval during the training session, also confirmed by exercise testing. After three months of detraining, no variation in the PR interval was observed. Echocardiography and cardiac magnetic resonance were normal, as well as genetic testing. Finally, we assessed the autoimmunity status of the patient and his mother, given the potential association between damage induced by anti-Ro/SSA antibodies and AV block and we found maternal seropositivity only, compatible with a late progressive congenital form of autoimmune AV bock. Accordingly, no circulating anti-Ro/SSA-autoantibodies were found in the athlete and we did not recommend immuno-modulating therapy. Considering the absence of symptoms and of cardiac, laboratory and genetic abnormalities, no circulating autoantibodies in the patient and the stability of the PR interval, the athlete was deemed eligible for sports competition. We advised him yearly follow-up visits to exclude the possibility of conduction disturbance progression. During the follow-up period he has continued to practice competitive sports without events. Discussion According to current recommendations, 1st degree AV block (up to 399 ms) and 2nd degree type 1 AV block can be considered physiological adaptations to exercise, especially if they disappear during exercise and detraining. Otherwise, further investigations are recommended to exclude abnormalities associated with sudden cardiac death in athletes, such as structural heart diseases, primary electrical diseases and autoimmunity. The most recognized form of autoimmune AV block is congenital (neonatal lupus). Growing evidence supports the existence of a late progressive congenital form, in which the conduction system injury is mediated by transplacental passage of antibodies produced by the mother and cross-reacting with calcium channels in the fetus, with a subclinical presentation in utero/at birth/in the neonatal phase and a manifest conduction disease later in life. Finally, autoimmune AV block can be acquired, in this case autoantibodies are found in the patient only and immuno-modulating therapy can be considered. In our case, maternal only seropositivity supported the hypothesis of a late progressive congenital form.