Natural killer (NK) cells can suppress the development of graft vs host disease (GVHD) while retaining antitumor response in allogeneic hematopoietic stem cell transplantation (allo-HSCT). Sphingosine-1-phosphate receptor 5 (S1PR5) can regulate NK cell migration and distribution in vivo by interacting with sphingosine-1-phosphate (S1P). This study was aimed to investigate S1PR5 expression change of NK cells in allo-HSCT and to explore the relationship between S1PR5 change and frequency of acute/chronic graft-versus-host disease (aGVHD/cGVHD). The S1PR5 expression was detected by real time quantitative PCR in the RNA extracted from blood NK cells of 17 couples of donor and recipient one month after allo-HSCT. The results showed that S1PR5 mRNA level variations in NK cells of donors and recipients post-allo-HSCT were not statistically significant (0.235 ± 0.191 vs 0.330 ± 0.261, P > 0.05). S1PR5 expression of NK cells was significantly lower in patients with aGVHD than those in patient without aGVHD (0.973 ± 0.834 vs 6.166 ± 5.32, P < 0.05). Compared with the corresponding donor, S1PR5 expression levels of patient declined by more than 10 that caused the high incidence of aGVHD. No significant correlation was found between S1PR5 expression of NK cells and cGVHD (3.401 ± 2.324 vs 2.762 ± 1.972, P > 0.05). It is concluded that the decreased expression level of NK cells S1PR5 is associated with aGVHD occurrence. Possible mechanism is due to S1PR5 low expression affecting distribution of NK cells in vivo, so affecting the regulation of NK cells for aGVHD.