Antibacterial therapy is the fundamental point in comprehensive treatment of patients with generalized periodontitis. The choice of an antibacterial drug, in view of its maximum effectiveness, is the key to successful pre-surgical preparation of patients with periodontitis to rapid post-surgery rehabilitation and remission maintenance. Our clinical study aims to analyze the activity of oral fluid enzymes (lactate dehydrogenase (LDH), alkaline phosphatase (ALP)) in patients treated with fluoroquinolones. 60 patients were allocated to groups. Each group had a 7-day course of one from four antibiotics: ciprofloxacin (250 mg; 2 times a day); ofloxacin (200 mg; 2 times a day); pefloxacin (400 mg; 2 times a day) and lincomycin hydrochloride (500 mg; 2 times a day). Ciprofloxacin was found to have the highest effect on the LDH and ALP suppression.