The cytolytic function of natural killer (NK) cells is controlled by a balance of activatory and inhibitory signals transduced by specific NK-cell receptors. NKG2 family is one of the superfamilies of these receptor genes located on chromosome 12 in the NKC gene complex. NKG2C is expressed as heterodimers with CD94 and they deliver activating signals upon contacting HLA-E via adaptor molecules. NKG2C genes are not only polymorphic and also NKG2C gene deletion was identified. The aim of the study was to develop a genotyping assay for the detection of the wild type and the deletion of the NKG2C gene. Method Copy numbers of the NKG2C genes were genotyped and assessed in 352 subjects by PCR-SSP method using a set of primer pairs described previously (Mararu M & Miyashita R, etc.). Two pairs of primers are used to detect the NKG2C genotypes: one pairs to amplify a 201 bp fragment from NKG2C wild type (wt) carrier; and the second pairs to amplify a 411 bp fragment from NKG2C deletion (del) carrier. A single-tube PCR-SSP genotyping strategy combining the two sets of primers was modified from Moraru M, etc. (Tissue Antigens, 2012). Results The presence or absence of NKG2C gene was determined by the single-tube PCR-SSP assay. Three genotypes were observed in the study subjects: wild type homozygous carrier (wt/wt), wild type and deletion heterozygous carrier (wt/del), and deletion homozygous carrier (del/del). Copy number of NKG2C in 3 International Histocompatibility Workshop (IHW) cells was assessed and confirmed: IHW 9043 as NKG2C wt/wt , IHW 9047 as NKG2C wt/del , and IHW 9044 as NKG2C del/del . Of the 352 subjects, wt/wt genotype accounted for 62.82% ( n = 221), wt/del for 32.88% ( n = 116), and del/del for 4.3% ( n = 15). The allele frequency of NKG2C deletion was 20.74% in this study group. Conclusion Studies have shown that NK cells expressing the activating receptor NKG2C preferentially expand after coculture with cytomegalovirus (CMV) infected fibroblasts and CMV-induced innate memory cells may contribute to malignant disease relapse protection and infectious disease control after transplantation. NKG2C deletion was shown to be a risk factor of HIV infection. Further study of the impact of the NKG2C CNV on outcomes of stem cell transplants with umbilical cord blood, related or unrelated donors would be warranted.