Treatment of reduced fertility in male dogs is often a great challenge for veterinarians. Infectious causes, alterations in the composition of the microbiome might also be in the background of impaired sperm quality. Although next-generation sequencing is becoming the most often used tool in studying the microbiome, our current knowledge is still scarce about the microbiome of the reproductive organ system of male dogs. Describing the normal microbiome of the genitals is essential for identifying pathogens and avoiding unnecessary antibiotic use. During our studies, we plan to compare the microbiome of the ejaculate, and the fraction obtained from the epididymis in case of animals kept under standard conditions or privately owned dogs, in parallel with ultrasound examination of the prostate and testicles and determination of sperm quality.