Azoospermia represents one of the most common reasons for infertility in the male. Although this finding is common in dogs, too, the underlying testicular changes are poorly characterised. We recently identified immune cell infiltration in 9 of 10 testicular biopsies from dogs suffering from non-obstructive azoospermia (NOA). Here, we aimed to obtain further insights into canine NOA (n = 10) by investigating the expression of the androgen receptor (AR) and the gap junction protein Connexin 43 (Cx43). Five healthy dogs with normal semen quality served as controls. Immunohistochemistry against AR and Cx43 was performed and evaluated including quantification of the immunopositive area (PIA) and the staining intensity (mean gray scale) by means of ImageTool 3.0. For AR, Sertoli, Leydig, peritubular and perivascular cells, and some spermatogonia were immunopositive. PIA and mean gray scale (p = 0.0013) were significantly lower in the tubuli of azoospermic dogs (PIA p = 0.0097; mean gray scale p = 0.0013), whereas only the mean gray scale differed significantly regarding interstitial AR expression (p = 0.0092) from the controls. For Cx43, immunopositive staining was found in the parabasal compartment within the Sertoli cell cytoplasm in the controls, but staining was diffuse in the tubuli of the azoospermic dogs. Neither PIA nor mean grey scale differed significantly between groups. Whereas especially tubular AR expression seems to be reduced in testes of azoospermic dogs compared to healthy controls, Cx43 distribution, but not quantity was affected in our samples indicating a disruption of the blood testis barrier. (We acknowledge funding of the GkF for this project.)