The predominant NK receptors recognizing MHC class I molecules are encoded by the killer cell immunoglobulin-like (KIR) genes in primates and the Ly49 genes in rodents. In human NK cells, the KIR repertoire is maintained epigenetically at the level of transcription via DNA methylation of the promoter region. We have previously shown a role for epigenetic mechanisms in the control of Ly49a transcription. However, it is unknown if all Ly49 genes are similarly regulated as they are diverged from each other in both DNA sequence and expression pattern. Ly49G is unstably expressed on EL4-derived sublines; some sublines lack expression while others such as RMA-E3 have substantial but variable expression. Here we show that transcription from the Pro-2 promoter of Ly49g is activated in an Ly49G-non-expressing EL4 subline after treatment with the histone deacetylase inhibitor, trichostatin-A. Ly49Ghigh RMA-E3 cells have significant hyperacetylation of the Pro-2 region compared to Ly49G− lymphoid and non-lymphoid cell lines. We hypothesize that the variable histone acetylation state at the Pro-2 region of Ly49g is responsible for the unstable and variable expression of Ly49G in the EL4 and RMA NKT cell lines. Histone acetylation may be the main epigenetic mechanism of transcriptional regulation for Ly49g in lymphoid cell lines and primary NK cells.