Sudden non-traumatic death in young athletes is due to underlying congenital/inherited cardiac diseases in over 80% of cases. The two commonest conditions leading to sudden cardiac death in athletes below the age of 25 years are hypertrophic cardiomyopathy (HCM) and arrhythmogenic right ventricular cardiomyopathy (ARVC). Hypertrophic cardiomyopathy is caused by mutations in genes, which code for sarcomeric contractile proteins. It can present with symptoms such as palpitation, presyncope or syncope. In a small number of cases, sudden death is the first clinical manifestation of the condition. It is well established that HCM accounts for over half of all cases sudden cardiac death in young individuals below 25 years of age. The management of HCM broadly encompasses symptom control, familial evaluation and the prevention of sudden death. Arrhythmogenic right ventricular cardiomyopathy, similarly, is a genetic disorder of the heart muscle and leads to symptoms such as palpitation and syncope and more rarely sudden death. The diagnosis of ARVC is most likely underestimated due to the lack of a single diagnostic test and subtle morphological changes in some cases. The diagnosis is based on clinical and family history and non-invasive investigations. The physiological adaptations seen in some athletes, as a response to physical training, may resemble phenotypically mild forms HCM and ARVC. Therefore, a diagnostic algorithm enabling this differentiation would be of importance especially bearing in mind the consequences of a misdiagnosis.