Evidence from genetic studies has revealed that genome-wide rare copy number variations (CNVs) are risk factors for neurodevelopmental disorders and this evidence has given rise to a new understanding of disease etiology, including that of schizophrenia (SCZ). Recent studies have indicated that duplication in the vasoactive intestinal peptide receptor-2 (VIPR2) gene confers the susceptibility to SCZ in Caucasians, but so far this finding has still not been confirmed in Chinese populations. In this study, we investigated the association between CNVs in VIPR2 and SCZ risk in an independent case-control study of Han Chinese using 1035 cases and 1535 controls. The CNVs were genotyped using the multiplex fluorescence competitive PCR method. In contrast with a common genotype (2-copy), a microduplication variant genotype (3-copy) was only carried by SCZ patients (4/1035). This finding indicated that CNVs in VIPR2 may impose a significantly increased risk of SCZ in Han Chinese (P=0.02646, OR=infinity, 95% CI=1.327-infinity). Thus, our results suggest that carriers of microduplication genotypes of VIPR2 are predisposed to SCZ in Han Chinese.