Atrial septal defect (ASD) is one of the most prevalent types of congenital heart disease (CHD). The pathogenic role of miRNAs in the development of ASD has not yet been fully elucidated. The aim of this study was to examine the miRNA profile of ASD patients, and to identify the role of miRNAs in the pathogenesis of ASD. We performed a miRNA comparison between the atrial septa of three normal fetuses and three ASD patients by microarray, followed by chromosome clustering and bioinformatic analysis to identify the dysregulated miRNA clusters between these two groups. Furthermore, qRT-PCR in the mouse developing heart was used to exclude differences resulting from the use of unpaired stage patient samples. After normalization, 70 dysregulated miRNAs were detected between the two groups. Advanced chromosome clustering and bioinformatic analysis showed that two upregulated miRNA clusters (miR-29 and miR-143/145) and three downregulated miRNA clusters (miR-17-92, miR-106b-25 and miR-503/424) were associated with ASD. Further qRT-PCR in the mouse developing heart found that the dysregulated expression levels of all the clusters, except the miR-143/145 cluster, were associated with the occurrence of ASD. This study reveals four dysregulated miRNA clusters, which will enable further elucidation of the pathogenic mechanism of ASD.