ZNF403 and LCRG1 are two alternative splicing isoforms from human gene ZNF403. Previous study shows that LCRG1 displays tumor-suppressive properties in laryngeal carcinoma cell line Hep-2 cells. The aim of this study is to clarify the relationships between these two isoforms and further investigate the role of ZNF403 in tumor cells. Realtime PCR analysis was first applied to demonstrate the relative abundance of these two isoforms and showed that ZNF403 is the major transcription product. The function of ZNF403 in cell growth was next accessed by MTT assay and tumor growth in nude mice analysis, respectively. The results indicated that ZNF403 knockdown resulted in inhibition of cell growth in Hep-2 cell both in vitro and in vivo. Moreover, bioinformatics analysis, flow-cytometric analysis and PCR array analysis were performed to elucidate the mechanism under the role of ZNF403 in cell growth. Knockdown of ZNF403 significantly decreased the rate of DNA synthesis and mitosis. Additionally, a number of key cell-cycle regulating components such as MCM2, p21, ATM and MRE11A were identified to be mediated by ZNF403. Altogether, our findings suggest that ZNF403 is a novel cell cycle regulator, which may play an essential role in tumorigenesis.