Background Matrix metalloproteinases (MMPs) are a family of host-derived proteinases reported to mediate multiple functions associated with periodontal destruction and inflammation. We have previously reported high MMP levels in African-American children with localized aggressive periodontitis (LAP). However, little is known about MMP reductions in gingival crevicular fluid (GCF) after therapy. This study aimed to evaluate MMP levels in the GCF following treatment of LAP and to correlate these levels with clinical response. Methods GCF samples were collected from 29 African-American individuals diagnosed with LAP. GCF was collected from one diseased site (pocket depth [PD]>4mm, bleeding on probing [BoP] and clinical attachment level [CAL] ≥2mm) and one healthy site (PD≤3mm, no BoP) from each individual at baseline, 3 and 6 months after periodontal treatment, which consisted of full-mouth SRP and systemic antibiotics. The volume of GCF was controlled using a calibrated gingival fluid meter and levels of MMP-1, 2, 3, 8, 9, 12 and 13 were assessed using fluorometric kits. Results MMP-1, 8, 9 12, and 13 levels were reduced significantly up to 6 months, at which point were comparable with healthy sites. Significant correlations were noted between MMP-2, 3, 8, 9, 12 and 13 levels and % of sites with PD>4mm. MMP-3, 12 and 13 levels also correlated with mean pocket depth of affected sites. Conclusion Treatment of LAP with SRP and systemic antibiotics was effective in reducing the local levels specific MMPs in African-American individuals, which correlated positively with some clinical parameters.