Aim Matrix metalloproteinases (MMPs) play a key role in the tissue destruction characteristic of chronic periodontitis. The purpose of this study was to investigate the association of MMP and TIMP polymorphisms with chronic periodontitis in two populations. Materials and Methods Thirty-four polymorphisms spanning 12 MMP and 2 TIMP genes were genotyped in 401 individuals from Brazil (99 cases with chronic periodontitis and 302 controls), and 274 individuals from the US (70 cases and 204 controls). Individuals were considered cases if presenting at least three teeth exhibiting sites of clinical attachment loss ≥5mm in two different quadrants. Controls were characterized by absence of clinical attachment loss and no sites with probing depth >3mm. MMP3 and TIMP1 mRNA expression was evaluated in healthy and diseased periodontal tissues. Results TIMP1 showed association with chronic periodontitis in the Brazilian population (for rs5906435, P=0.0004), whereas MMP3 showed association in the US population (for rs679620, P=0.0003; and rs650108, P=0.002) and in the Brazilian population (for rs639752, P=0.005). MMP3 and TIMP1 mRNA expression was significantly higher in diseased tissues when compared to control tissues. Conclusions Our results further support a role for variations in MMP3 in chronic periodontitis and report a novel association with TIMP1. These genes may be considered additional candidate genes for chronic periodontitis.