MicroRNAs (miRNAs) are small non-coding RNAs that control patterns of gene expression by inducing the degradation of mRNAs. In addition, miRNAs are known to serve an important role in the pathogenesis of atrial fibrillation (AF). In general, AF is diagnosed using electrocardiography. However, the present study investigated whether specific miRNAs derived from microarray analysis of human urine could regulate AF through the inhibition of calcium handling protein phosphorylation in an AF model. Microarray analysis of the transcriptome in the human urine of patients with paroxysmal supraventricular tachycardia and AF revealed that 7 differentially expressed miRNAs were significantly downregulated (miR-3613, 6763, 423, 3162, 1180, 6511, 3197) in patients with AF. In addition, quantitative PCR results demonstrated that collagen I, collagen III, fibronectin and TGF-β, which are fibrosis-related genes, were upregulated in patients with AF. Furthermore, fibrosis-related genes were upregulated in angiotensin II-induced atrial myocytes, which demonstrated that these genes may be targets of miR-423. In the AF cell model transfected with miR-423, the expres- sion of calcium handling proteins, including phosphorylated calmodulin-dependent protein kinase II, was reduced. The transfection of miR-423 attenuated damage to cardiac cells caused by calcium handling proteins. The findings highlight the importance of calcium handling protein phosphorylation changes in fibrosis-induced AF and support miR-423 detection in human urine as a potential novel approach of AF diagnosis.