Mitochondrial respiratory chain disorders (MRCD) are a heterogeneous group of diseases leading to an inadequate production of ATP. Brain and heart are among the most affected organs. Thus far, no specific relationship has been found between specific affected areas in the central nervous system and cardiac involvement. This study investigated the relationship between specific brain involvement and heart disease in mitochondrial disorders. We hypothesize that specific areas of brain lesions in children with MRCD are more frequently correlated to heart disease than others. A retrospective evaluation of the clinical records of 63 children with a definite MRCD, was performed searching for heart disease, namely, dilated and hypertrophic cardiomyopathy and arrhythmia. Brain MR images were evaluated and characterized regarding specific areas of atrophy and involvement. These findings were correlated using the Fischer exact test whose strength was determined with the Phi coefficient. During the period analyzed, 13 children (20.6%) developed cardiac disease, of whom nine (14.3%) exhibited isolated cardiomyopathy, one (1.6%) exhibited arrhythmia and three both. The main MRI abnormalities observed were brain atrophy (65.1%) and among this group 17.5% of subjects had cerebellar involvement. In addition, supratentorial, cerebellar and brainstem white and grey matter lesions were also found. There was a statistically significant relationship between progression to cardiac disease and cerebellar atrophy (Fisher's Exact Test -0.005 and Phi 0.394) and lesions in the cerebral peduncles (0.035/0.358). Moreover, there was an additional correlation between thalamic lesions and progression to hypertrophic myocardiopathy (0.029/0.397). A statistical relationship between thalamic, mesencephalic and cerebellar involvement and cardiac disease in children with definite MRCD was observed. The true significance of this connection warrants further assessment.