Novel single nucleotide polymorphisms in the human bone gamma carboxyglutamate protein (BGLAP) gene are described. In addition, various genotypes, haplotypes and haplotype pairs for the BGLAP gene that exist in the population are described. Compositions and methods for haplotyping and/or genotyping the BGLAP gene in an individual are also disclosed. Polynucleotides containing one or more of the BGLAP polymorphisms disclosed herein are also described.