Background: microRNAs are crucial for cardiovascular development and are associated with congenital heart disease (CHD). Recent studies have shown that microRNAs play a role in heart development and is closely related to CHD. The present study investigated the underlying mechanism of microRNA-208a (miR-208a) in "simple" CHD. Material and Methods: Reverse transcription-quantitative PCR (RT-qPCR) demonstrated miR-208a expression levels in children with CHD (n = 27) compared with normal controls (n = 29), in cardiomyocytes from embryo 10 (E10) to post-birth (P7) and organs in adult rats in healthy rats. Apoptosis of H9c2 cells after transfection with miR-208a detected by TUNEL assay. B-cell lymphoma (Bcl)-2, an anti-apoptotic gene, was detected by RT-qPCR, as well as Gata4. After 48h overexpression of miR-208a, GATA4 was detected via western blotting. Dual luciferase reporting system was used to identify the binding sites of miR-208a to Gata4. Results: Expression of miR-208a was upregulated in the CHD group via the control group (p < 0.01). At P7, miR-208a had the highest expression (p < 0.01), and which was highest in myocardiocytes via other organs or tissues (p < 0.01) in adult rats. The number of apoptotic cells increased significantly post-transfection with miR-208a (p < 0.01), while decreased with the miR-208a inhibitor via the control group (p < 0.01). Compared with the control group, there was no significant difference in the expression level of Bcl-2 after miR-208a overexpression (p > 0.05). The present study proved that miR-208a binds directly to the 3´-UTR of Gata4 at site 1,363-1,369 bp. Expression of GATA4 decreased after miR-208a overexpression (p < 0.01), but increased following transfection with a miR-208a inhibitor via the control group (p < 0.05). Conclusions: Our study demonstrated that miR-208a downregulates Bcl-2 by directly targeting GATA4, which may cause CHD. miR-208a may become a new biomarker or therapeutic target for CHD in the future.