We previously reported clinical and radiological findings in a Belgian family with a complex type of synpolydactyly associated with metacarpal and metatarsal synostoses, cosegregating with a balanced t(12;22). Recently, expansions of a polyalanine stretch within the first exon of the HOXD13 gene, which resides on chromosome 2q31, have been shown to cause synpolydactyly (SPD). Using exon amplification followed by direct sequencing, we were able to exclude the direct involvement of the HOXD13 gene in this family. As a first step toward the positional cloning of a candidate disease gene on chromosome 12 and/or 22 responsible for the type of complex synpolydactyly observed in this family, we report here the construction of a somatic cell hybrid retaining only the der(22) of the t(12;22)(p11.3;q13.3). STS content mapping and FISH experiments allowed us to position the chromosomal breakpoints between markers D12S1596 and D12S1034 on chromosome 12 and markers N73F4 and D22S158 on chromosome 22.