ABSTRACT Chromatin rearrangements in the meiotic prophase are characterized by the assembly and disassembly of synaptonemal complexes (SC), a protein structure that stabilizes the pairing of homologous chromosomes in prophase. We report the identification of human and mouse cDNA coding for stromalin 3 (STAG3), a new mammalian stromalin member of the synaptonemal complex. The stroma‐lins are a group of highly conserved proteins, represented in several organisms from yeast to humans. Stromalins are characterized by the stromalin conservative domain (SCD), a specific motif found in all proteins of the family described to date. STAG3 is expressed specifically in testis, and immunolocalization experiments show that STAG3 is associated to the synaptonemal complex. As the protein encoded by the homologous gene (Scc3p) in Saccharomyces cerevisiae was found to be a subunit of a cohesin complex that binds chromosomes until the onset of anaphase, our data suggest that STAG3 is involved in chromosome pairing and maintenance of synaptone‐mal complex structure during the pachytene phase of meiosis in a cohesin‐like manner. We have mapped the human STAG3 gene to the 7q22 region of chromosome 7; six human STAG3‐related genes have also been mapped: two at 7q22 near the functional gene, one at 7qll.22, and three at 7qll.23, two of them flanking the breakpoints commonly associated with the Williams‐Beuren syndrome (WBS) deletion. Since the WBS deletion occurs as a consequence of unequal meiotic crossing over, we suggest that STAG3 duplications predispose to germline chromosomal rearrangement within this region.—Pezzi, N., Prieto, I., Kremer, L., Pérez Jurado, L. A., Valero, C., del Mazo, J., Martínez‐A., C., Barbero, J. L. STAG3 , a novel gene encoding a protein involved in meiotic chromosome pairing and location of STAG3 ‐related genes flanking the Williams‐Beuren syndrome deletion. FASEB J. 14, 581–592 (2000)