The expression of the transmembrane neuronal gap junction protein connexin 36 (Cx36) was investigated in the reticulo-thalamic nucleus (RT) and in the CA3 region of hippocampus in a rat model of Parkinson’s disease (PD). We compared the Cx36 expression in a rat model of PD (the hemiparkinsonian rats with PD cholinopathy - unilateral lesion of the substantia nigra pars compacta (SNpc) with bilateral lesion of the pedunculopontine nucleus (PPT)) versus control rats.A total of 12 adult male Wistar rats were divided in control group (n = 6) and PD group (n = 6). We performed a fluorescence immunohistochemistry protocol for Cx36 staining on free floating 40-µm brain slices. For quantification of the positive Cx36 immunofluorescence labeling we used tiff images (scale 50 µm). We calculated the mean value of integrated density (ID) for each brain side of each experimental group using ImageJ software.We observed a significant and uniform suppression of Cx36 staining in the CA3 region, on both the SNpc/PPT and PPT lesioned sides in the PD group (X2 = 7.54, p = 0.02; z = -1.36, p = 0.22), compared to the control brains (z = -2.24, p = 0.04). For RT, a statistically significant suppression was found only on the SNpc/PPT lesion side compared to the control brain side and the PPT lesion side (X2 = 8.35, p = 0.02; z = -2.31, p = 0.03).Differential expression of Cx36 in the RT and hippocampus suggests its different local expression related to underlying PD neuropathology.