Natural killer (NK) and T‐lymphocytes monitor human leukocyte antigen (HLA)‐E expression through CD94:NKG2 heterodimers. Structural polymorphism is not a hallmark for NK‐complex genes on chromosome 12, except for complete NKG2C deletion in some humans. We present a method for fast, simple and accurate assessment of NKG2C copy‐number variation – presence or absence in the genome of an NKG2C gene, in homo‐ or heterozygosis, is detected by a single conventional polymerase chain reaction that yields amplicons of different lengths in each genotype. We have also determined the NKG2C genotypes of a reference cell panel comprising 13 NK‐ and tumour‐cell lines and 39 Epstein‐Barr virus transformed cells from the International Histocompatibility Workshop. Our results should facilitate research on the importance of NKG2C and its deletion for immunity.