Recent evidence indicated that the PRKCH gene was a susceptibility gene for lacunar infarction in a Japanese population. The aim of the present study was to explore the association of the gene with lacunar infarction in a population of Chinese Han ancestry. A total of 280 consecutive lacunar infarction patients and 306 unrelated population-based controls that had been matched for age and sex were examined using a case-control design. Two single nucleotide polymorphisms (SNPs) of PRKCH gene (rs3783799 and rs2230500) were genotyped with ligase detection reaction (LDR) and multiplex polymerase chain reaction (PCR). Linkage disequilibrium (LD) and haplotype analysis were also investigated between these two groups. Overall alleles and genotype frequencies were similar between cases and controls. No significant association was detected with the gene polymorphisms mentioned above and lacunar infarction; no significant difference was found with haplotype analysis between these two groups. None of the two SNPs showed significant association with lacunar infarction in the whole subjects before and after adjustment for conventional stroke risk factors (hypertension, diabetes mellitus, and hypercholesterolemia). The frequencies of PRKCH differed largely from those in the Japanese population. The present study suggests that variants in the PRKCH gene are not the risk factors for lacunar infarction in individuals from a small population of Chinese Han ancestry. Population differences in alleles and haplotype frequencies as well as LD structure may contribute to the observed differences between populations.