Objectives To investigate the relationship between coronary artery calcification and calcium deposition in cardiomyocytes. Methods Patients who underwent valve replacement plus surgical ablation for atrial fibrillation, together with left atrial appendage resection, were included. Coronary artery calcification (CAC) score was evaluated prior to surgery using dual-source computed tomography. Samples of left atrial appendage tissue were collected to analyse the following indicators: calcium deposition, alkaline phosphatase activity, calcium content, protein levels of runt-related transcription factor 2 (Runx2), osteopontin and beta-catenin, and mRNA levels of osteopontin, endothelin and ghrelin. Relationships between CAC score and various indicators were analysed by univariate logistic or linear regression. Results Out of tissue from eight patients, CAC score was not correlated with cardiomyocyte calcification (odds ratio [OR] 0.984 and OR 0.983; von Kossa or alizarin red staining, respectively). CAC score showed an inverse linear correlation with Runx2 protein (beta = -0.75), but was not correlated with osteopontin (beta = -0.52) or beta-catenin protein (beta = -0.56), mRNA levels of osteopontin, endothelin and ghrelin (beta = 0.13, 0.02, and 0.02, respectively), alkaline phosphatase activity (beta = 0.56), or calcium content (beta = -0.22). Conclusions Coronary artery calcification was not correlated with calcium deposition in cardiomyocytes.