Abstract Criss-cross heart is a rare congenital cardiac defect characterized by crossing of the atrioventricular valves and of the inflow streams due to the twisting of the ventricles about their long axis. The aetiology of criss-cross heart has not been understood yet. Mice homozygous for Cx43 deficiency show a delay in normal looping of ascending limb of the heart tube, which temporarily retains a more symmetric middle position. Persistence of this condition results in a “criss-cross” configuration, with the atrioventricular cushions rotated 90°, a horizontal muscular ventricular septum, and a parallel course of the endocardial ridges of the outflow tract. We screened the entire coding region of the Cx43 gene in a group of well characterized patients with criss-cross heart, to evaluate whether Cx43 gene mutations cause criss-cross heart in humans. No pathogenic mutation was identified, suggesting that Cx43 mutations are not responsible for criss-cross heart in humans or are not a major cause for this defect.