Green fluorescent proteins (GFP), extensively used as reporters in biological and imaging studies, are assumed to be mostly biologically inert. Here, we test the assumption in regard to the transcriptional regulation of 18 mitochondrially encoded genes in GFP expressing human T-cell line (JURKAT cells) exposed to gamma radiation. Using quantitative polymerase chain reaction, we demonstrate that wild type and GFP expressing JURKAT cells have different baseline mitochondrial transcript expression (10 out of the 18 tested genes) and after a single dose of radiation (100 Gy) show a significantly different transcriptional regulation of their mitochondrial genes. While in wild type cells, ten of the tested genes are up-regulated in response to radiation exposure, GFP expressing cells show less transcriptional regulation with a small down-regulation in five genes. Our results indicate that the presence of GFP in the cytoplasm can alter the cellular response to ionizing radiation.