Bisphosphonates represent a class of pharmacologic agents that have a potentially important role in the treatment of periodontitis and bone disorders. The present study aims to explore the clinical efficacy of 1% alendronate (ALN) gel as a local drug delivery system in adjunct to scaling and root planing for the treatment of patients with aggressive periodontitis (AgP) compared to placebo gel. Fifty-two intrabony defects from 17 patients with AgP were treated either with 1% ALN gel or placebo gel. ALN gel was prepared by adding ALN to a polyacrylic acid-distilled water mixture. Clinical parameters (modified sulcus bleeding index, plaque index, probing depth [PD], and clinical attachment level [CAL]) were recorded at baseline, 2 months, and 6 months, and radiographic parameters were recorded at baseline and 6 months. Defect fill at baseline and at 6 months was calculated on standardized radiographs by using image analysis software. Mean PD reduction was greater in the ALN group (3.88 ± 1.39 mm) compared to placebo (1.65 ± 1.35 mm) at 6 months. Similarly, mean CAL gain was greater in the ALN group (3.27 ± 1.11 mm) than the placebo group (1.42 ± 1.70 mm) at 6 months. Furthermore, significantly greater mean percentage of bone fill was found in the ALN group (46.1% ± 9.48%) compared to the placebo group (2% ± 1.02%). The results of the present study show local delivery of 1% ALN stimulates a significant increase in PD reduction, CAL gain, and improved bone fill compared to placebo gel as an adjunct to scaling and root planing in patients with AgP. However, long-term, multicentered, randomized, controlled clinical trials are required to know the clinical, histologic, and radiographic effect on bone regeneration in patients with AgP.