In addition to showing a significant association at the individual locus level, the current study, and for the very first time, shows a strong association between IL-1 polymorphisms and sever chronic periodontitis based on bi-locus haplotype analysis and LD contrast between cases and control; a properiodontitis (T-T) and an antiperiodontitis (C-T) haplotypes were identified, and a significant LD was observed in cases but not in controls. This evidence concerns the gene IL1B and chronic periodontitis.