The cytogenetic expression of the FRAXF fragile site is due to an expanded, hypermethylated and unstable CGG repeat in Xq28. Normal individuals have 6-38 triplet repeats while individuals expressing the fragile site have expansions of greater than 300 triplets. Through analysis of the region adjacent to the fragile site, we have identified a approximately 2.6 kb cDNA originating from the FRAXF fragile site associated CpG island, and containing the unstable FRAXF CGG repeat in its 5' UTR region. This gene, FAM11A, comprises at least seven exons, shows alternative splicing, and extends over 35 kb of genomic DNA distal to the FRAXF fragile site. Analysis of the FAM11A cDNA sequence has identified a 1050 bp open reading frame encoding a 350 amino acid protein. We have also identified FAM11B a highly conserved (88% at the protein level) transcribed chromosome 2 retropseudogene. We show that the novel FRAXF fragile site associated gene FAM11A is transcriptionally silenced in a normal individual with a cytogenetically and molecularly detectable FRAXF CGG full mutation (fragile site). Finally, we were able to reactivate FAM11A transcription by treatment of a FRAXF lymphoblastoid cell line with the demethylating agent 5-azadeoxycytidine, thus demonstrating the critical role of FRAXF methylation in FAM11A silencing.