Periodontal disease is one of the most common canine diseases that can have serious systemic consequences. The aim of the study was the identification of the bacterial microflora causing periodontitis as well as its influence on the pathological changes in heart and kidneys. The study was performed on the group of 19 dogs (10 males and 9 females, aged between 6-15 years) sectioned at the Pathological Anatomy Department in Lublin, Poland. In all dogs the periodontal disease (third stage in 5 dogs and the fourth stage in 14 dogs) was diagnosed. A culture of aerobic bacteria from clinical material (swab of gingival, heart and kidneys) and histopathological examination on heart and kidney were performed. In the material the presence of bacteries such as: Escherichia coli, Streptococcus spp., Streptococcus pyogenes, Streptococcus equi, Staphylococcus epidermidis, Staphylococcus spp. and Corynebacterium spp. The results of this study showed the advanced pathological changes in kidney glomeruli and the anterior wall of the left heart in all animals, especially in the dogs with the fourth stage of periodontitis. In histopathological examination of preparations from the anterior wall of the left heart ventricle the intense interstitial cardiac oedema and interstitial fibrosis was diagnosed. Additionally, subepicardially between the muscle fibres and around the vessels single adipocytes were found. The study reveals the important correlations between chronic inflammatory lesions within periodontal tissues and heart and kidneys.