Matrix metalloproteinases (MMPs) are involved in periodontal tissue remodeling and degradation. MMP polymorphisms could alter transcription and function of these enzymes. The aim of this study was to investigate MMP-2, MMP-9 and MMP-12 gene polymorphisms in relation to susceptibility to severe chronic periodontitis (CP).Genomic DNA was obtained from peripheral blood of 87 severe CP patients and 107 periodontally healthy subjects. MMP-2 −735C/T, MMP-9 −1562C/T and MMP −12357Asn/Ser gene polymorphisms were genotyped by polymerase chain reaction and restriction fragment length polymorphism. Probing depth, clinical attachment loss, supragingival plaque accumulation and bleeding on probing were recorded. The data were analyzed by chi-square, logistic regression and Mann–Whitney-U-tests.The genotype distributions and allele frequencies of MMP-2, MMP-9 and MMP-12 genes were similar in CP and healthy subjects (p > 0.05). Differences between rare allele carriage rates of CP and healthy groups regarding MMP-2, MMP-9 and MMP-12 gene polymorphisms were not significant (p > 0.05). However, T allele carriers of MMP-9 −1562 gene had less risk for CP (OR = 0.36; 95% CI = 0.16–0.81).These data suggest that MMP-2 −735C/T, MMP-9 −1562C/T and MMP-12 357Asn/Ser polymorphisms are not associated with susceptibility to severe CP in Turkish population. However, T allele of MMP-9 −1562 gene might be associated with decreased susceptibility to severe CP.