In 28 adult severe periodontitis patients who did not respond to conventional periodontal therapy, full mouth clinical parameters including probing pocket depth, relative attachment level, bleeding on probing and suppuration after probing, visible plaque index and modified gingival index were recorded at the baseline and 14 months after treatment. Based on clinical and bacteriological diagnosis, a combination of systemic amoxicillin 500 mg x 3 and metronidazole 200 mg x 2 was prescribed for 7 days. In combination with non-surgical treatment, systemic antibiotic therapy, significantly improved median values of probing pocket depth, bleeding on probing, suppuration index, visible plaque index and modified gingival index except relative attachment level. Despite the improvement of clinical parameters in general, both bleeding on probing and suppuration index had significantly lower reduction in smokers than in non-smokers.