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Background: A previous study on the genetic association between single nucleotide polymorphisms in FGFR1OP2/wit3.0 and the long term atrophy of edentulous mandible hypothesized that the excessive jawbone atrophy after dental extraction may be associated with abnormal oral mucosa contraction induced by the FGFR1OP2/wit 3.0 gene. It was reported that the minor allele of rs840869 or rs859024 in FGFR1OP2/wit3.0 was associated with the excessive atrophy of edentulous mandible. The present study represents an attempt to replicate the results of this previous study and to examine the genetic association between polymorphisms in FGFR1OP2 and residual ridge resorption of mandible in a Korean population. Methodology/Principal Findings: 134 subjects (70.46±9.02 years) with partially or completely edentulous mandible were recruited. The mandibular bone height was measured following the protocol of the American College of Prosthodontists (ACP). From 24 subjects, seven variants in FGFR1OP2 were discovered and four of them were novel. Selected SNPs that are not in high LD at r2 threshold of 0.8 were genotyped for the remaining population. There was no frequency of the minor allele of SNP rs859024 in Korean population. SNP rs840869 was not associated with residual ridge resorption (p = 0.479). The bone height of the subject with the ss518063493 minor allele (8.52 mm) was shorter than that of those subjects with major alleles (18.96±5.33 mm, p = 0.053). Conclusions/Significance: The patient with minor allele of ss518063493 may be associated with excessive atrophy of edentulous mandible whereas the patients with that of rs840869 are not associated in Korean population. The result from this study may assist in developing a novel genetic diagnostic test and be useful in identifying Koreans susceptible to developing excessive jawbone atrophy after dental extraction. [ABSTRACT FROM AUTHOR]