This study was designed to evaluate the clinical significance of antibiotic therapy combined with guided tissue regeneration (GTR) therapy with a collagen membrane. The subjects were 20 adults diagnosed with periodontitis (20 intrabony periodontal defects). Ten patients were treated with GTR alone (control group) and the other 10 patients were treated with a combination of GTR and antibiotics (antibiotic group). In the antibiotic group, minocycline ointment was applied locally before GTR therapy, and doxycycline and amoxyline were systemically administered after GTR therapy. Clinical manifestations, the presence or absence of exposed membrane, and microbiological findings were assessed 1 month before, immediately after, and 2 weeks, 6 weeks, and 3 months after GTR therapy. The results showed no significant differences in reduction of probing depth, probing attachment gain (PAG), or the ratio of PAG to intraoperative depth of the intrabony defect (vertical relative attachment gain) between the antibiotic group and the control group before and 3 months after GTR therapy. A DNA probe test and specific enzymatic activity test revealed no significant differences in the improvement and the rate of bacterial negativity before, and 6 weeks and 3 months after, GTR therapy. These findings indicate that antibiotic therapy is not clinically beneficial when combined with GTR therapy with a collagen membrane.