Introduction: Analysis of progression rate of periodontal disease indicates individual variability. It should be noted that destructive event in the alveolar bone has been linked to homocysteine (Hcys) metabolism; however, the issue has not yet been fully studied. Objectives: To assess the peculiarities of the process of peripheral blood neutrophils programmed death in rats with lipo-polysaccharide (LPS)-induced periodontitis combined with chronic thiolactone hyper-homocysteinemia (HHcy). Material and methods: 48 mature inbred white male rats were divided into four groups: control (n = 12), LPS-induced periodontitis (n = 12), chronic thiolactone HHcy (n = 12), and LPS-induced periodontitis combined with HHcy (n = 12). Analysis of peripheral blood neutrophil samples to determine all the studied parameters was performed on flow cytometer Epics XL (Beckman Coulter; USA). Results: LPS-induced periodontitis in rats was accompanied by reactive oxygen species (ROS) hyper-production (by 87.9%, p = 0.001) and trans-membrane mitochondrial potential decrease by 73.3% (p = 0.001), which resulted in the distortion of integrity of the outer mitochondrial membrane, and the initiation of apoptotic events. Chronic thiolactone HHcy enhanced the initiation of the programmed death of neutrophils in case of LPSinduced periodontitis, which was confirmed by 71.4% significant prevalence of the apoptotic cells in animals with LPS-induced periodontitis combined with chronic thiolactone HHcy vs. rats with only LPS-induced periodontitis. Conclusions: Excessive production of ROS and mitochondrial dysfunction caused by high serum Hcys level can be a crucial molecular mechanism that enhances programmed cell death in rats with LPS-induced periodontitis combined with chronic thiolactone HHcy, which opens opportunities to improve pathogenetic therapy in patients with comorbid course of periodontal disease and chronic HHcy.