Background: Periodontitis is characterized as a chronic inflammatory disease. Periodontopathogens induce innate responses amongst others via CD14, TLR 2 and 4 resulting in activation of NF-kB. Functional important SNPs are described for these genes. The aim of this study was to evaluate links between SNP and the subgingival occurrence of periodontopathogens. Patients and Methods: 141 periodontitis patients and 81 healthy controls without periodontitis were included in the study. SNPs in CD14 (c.-159C>T), in TLR4 (Asp299Gly, Thr399Ile), in TLR2 (Arg677Trp, Arg753Gln), and in NF-kB (-94ins/delATTG) were determined by RFLP. Subgingival bacterial colonization was analysed molecularbiologically using the micro-Ident®test. Results: Associations between genotype and the occurrence of periodontopathogens could be shown: Heterozygous carriers of the Arg753Gln SNP in TLR2 are at a higher risk for the occurrence of bacteria of the "red complex" (p=0.042). P. intermedia occurred less frequently in individuals positive for the TT genotype of CD14 (p=0.045). Homozygous del/del carriers of the NF-kB SNP had a higher risk for subgingival colonization with A. actinomycetemcomitans (p=0.031). In binary logistic regression analyses, the associations for SNP in CD14 (OR=3.22, CI: 1.23-8.33, p=0.017) and NF-kB (OR=2.7, CI: 1.04-6.98, p=0.042) could be proven considering age, gender, smoking, and clinical attachment loss or approximal plaque index, respectively, as confounding factors. No genotype dependent association with subgingival occurrence of periodontopathogens could be proven for SNPs in TLR4 and TLR2 (Arg677Trp). Conclusions: SNPs in candidate genes responsible for the bacterial recognition and elimination could be shown to be associated with the subgingival occurrence of periodontopathogens. The analysis of the disease related genetic pattern may help to identify early persons at high periodontal risk and improve the success of the periodontal therapy. Keywords: periodontitis, periodontopathogens, CD14, TLR2, TLR4, SNP