Pharmacogenetic studies have confirmed that the genetic variant of the casein kinase 1 epsilon (Csnk1ε) gene contributes to response variability to amphetamine and methamphetamine in both mice and humans. A polymorphism in the Csnk1ε gene has been reported to be associated with heroin dependence. In this study, to identify markers contributing to the genetic susceptibility of the Csnk1ε gene to heroin dependence, we examined the potential association between heroin dependence and 14 single nucleotide polymorphisms (SNPs; rs1997644, rs135764, rs867198, rs135763, rs135757, rs6001090, rs5750581, rs1534891, rs1005473, rs3890379, rs2075984, rs2075983, rs135749, and rs135745) of the Csnk1ε gene using the MassARRAY system. Participants included 398 heroin-dependent patients and 436 healthy controls from a Han Chinese population. The result revealed a strong association between the rs135745 (3'-untranslated region) genotype distribution and heroin dependence (P = 0.0006). The frequency of the C allele was significantly higher in the heroin-dependent patients than in the healthy controls (χ(2) = 7.172, P = 0.007, OR = 1.426, 95 % CI = 1.099-1.849). Further genotype and clinical phenotype correlation study of the rs135745 carriers showed that the amount of heroin self-injection was higher in patients with the GC + CC genotype compared to the patients with the GG genotypes (P < 0.01). Strong linkage disequilibrium (LD) was observed in block 1, block 2, and block 3 (D' > 0.9), whereas significant evidence of LD was not observed between these SNPs in our sample population. These findings point to a role for Csnk1ε polymorphisms in heroin dependence among the Han Chinese population and may be informative for future genetic or neurobiological studies on heroin dependence.