Programmed cell death 1 (PD-1) has recently been reported to have a genetic association in several autoimmune diseases. The object of this study was to investigate the association of PD-1 polymorphisms with aplastic anemia (AA) in the Chinese Han population. In a case-control association study, three single-nucleotide polymorphisms (SNP), PD-1.3 G/A, PD-1.5 C/T, and PD-1.9 T/C, were genotyped in 166 AA patients and 264 healthy controls using polymerase chain reaction-restriction fragment length polymorphism assay. All genotype distributions in the patients and the controls were in Hardy-Weinberg equilibrium. The associations of genotypes and alleles with AA were analyzed. No differences in genotype and allele frequencies were elucidated for SNPs in intron 4 and exon 5. In conclusion, we show no association of selected SNPs in PDCD1 gene with AA in the Chinese Han population.