Converging evidence from imaging, microarray, genetic, and other studies suggests that abnormalities in myelin may play a role in schizophrenia. The expression of 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP), which is used as a myelin marker, has been reported to be reduced in the schizophrenic brain. A synonymous genetic variation in the CNP gene, rs2070106, has recently been shown to be associated with schizophrenia in Caucasians. The present study investigates whether this finding can be replicated in the Han Chinese population. We performed an association analysis of four ht-SNPs in the CNP gene in a Chinese sample consisting of 426 schizophrenic patients and 439 healthy controls. We did not find any significant differences in any genotypic, allelic or haplotypic distributions between patients and controls. Therefore, this study did not find an association between genetic variations in the CNP gene and schizophrenia in the Han Chinese population.