In heart, Kir6.2 is responsible for the ATP-sensitive K⁺ current (I_KATP) and Kir2.1 is in part responsible for the background inward rectifier K⁺ current (I_K1). In this study, transgenic mice expressing either GFP-tagged Kir6.2 or Kir2.1 K⁺ channel subunits under the control of the cardiac α-myosin heavy chain (α-MHC) promoter were generated. We have investigated the distribution in humanely killed mice of Kir6.2-GFP and Kir2.1-GFP mRNA in the sinoatrial node (SAN), compact atrioventricular node (AVN), His bundle, and working myocardium from these transgenic mice. Digoxigenin labelled sense and anti-sense riboprobes were made specific for GFP, and in situ hybridisation was carried out on 10 μm tissue sections mounted on glass slides. We observed that Kir6.2-GFP mRNA was expressed in the SAN (n=3), atrium (n=3) and ventricle (n=3) of transgenic hearts, but was absent in the compact AVN (n=3) and His bundle (n=3). Kir2.1-GFP mRNA was expressed in the atrium (n=3) and ventricle (n=3), but was absent in the SAN (n=3), compact AVN (n=3) and His bundle (n=3). No Kir6.2-GFP and Kir6.2-GFP mRNA was observed in tissue sections from non-transgenic mice from the same litter. The presence or absence of Kir6.2-GFP and Kir2.1-GFP mRNA in the SAN, AVN, His bundle, atrium and ventricle faithfully follows the presence or absence of Kir6.2-GFP and Kir2.1-GFP proteins in these heart tissues. These patterns do not correspond to the expected distribution of α-MHC mRNA, whose core promoter was used in the construct. They do, however, largely correspond to the expected distribution of Kir6.2 and Kir2.1 mRNA and protein in the SAN, AVN and His bundle. This suggests transcriptional regulation of the genes, i.e. control at the level of the transcript, leading to directed exclusion of both transcript and protein from the specific conducting tissues. This may be an important mechanism controlling the expression of the wild-type Kir6.2 and Kir2.1 genes.