In a previous linkage study, suggestive linkage to osteoporosis was observed in marker D11S1392 on chromosome 11p12. The CD44 gene, found at this locus, was sequenced in one of the families studied. Sequencing all coding regions and promoter in affected and non-affected family members revealed a number of sequence variants, one of which was found to be linked and inherited identical by descent together with the linked STR allele. This G to A variant, which does not cause an amino acid change, was found in exon 9 of the CD44 gene, 32 base pairs upstream from the exon-intron junction. Preliminary analysis using a bioinformatics tool suggested that the presence of the A allele abolished an exon splicing enhancer (ESE) site, thus possibly affecting RNA splicing. It was observed using an exon-trapping vector, that in the presence of the A allele, only one transcript was observed in RAW264.7 cells, as opposed to two transcripts transcribed in the presence of the G allele. These observations suggest that the linked synonymous variant found in exon 9 of the CD44 gene might be increasing susceptibility to osteoporosis in this family by affecting the splicing mechanism.