DPD enzyme, encoded by the DPYD gene, is the major rate-limiting enzyme in the metabolism of the anti-cancer drugs. And it exists substantial inter-individual variations in its enzymatic activity. It was shown that mutant alleles of DPYD that encoding an inactive/decreased enzyme are largely caused by SNP (single nucleotide polymorphism) in the gene. Detection of the SNPs is the basis for the prediction of drug-response and realization of individualized therapeutic regimen for patients. For this reason an oligonucleotide microarray for genotyping 6 known SNPs of DPYD gene was optimized, and the genotyping standard for this microarray was fabricated. The microarray system was used to detect the mutant allelic frequency of DPYD in cancer patients (112 individuals), nephrotic patients (83 individuals) and healthy subjects(45 individuals). In the studied groups, the average frequencies for the mutant alleles of DPYD^*5 and DPYD^*9 are 11.25% and 32.08% respectively. No mutant alleles of DPYD^*2, ^*3, ^*4, ^*12 were found. And there is no significant difference (P＞0.05) in the mutation incidence in different subject groups or sex groups. The SNPs was shown to have no significant association with the disease and sex. The genotyping results of 20 samples were tested by direct sequencing, the genotyping results of 19 samples by miroarray were conformed with the direct sequencing. The allelic frequencies of DPYD^*5 and DPYD^*9 is high in the studied groups, quick and accurate detection of them can be achieved by using DNA microarray.