Chromosome specific cDNA libraries are a useful source of candidate genes for disorders which have been linked to particular chromosomes. Here, we report the generation of a cDNA library made from a somatic cell hybrid retaining chromosome 6 as its only human component. In order to ascertain the chromosomal location of cDNAs the library was amplified by inter-Alu-PCR and used as probe for competitive in situ suppression (CISS). To identify human specific cDNA clones the library was screened with PD39, a highly human specific Alu consensus probe. Out of 350,000 clones 360 were found to hybridize with PD39. Nucleotide sequences were determined for 40 clones with inserts larger than 500 basepairs (bp) and a sequence comparison was performed at the National Center for Biotechnology Information using BLASTN. One clone was shown to be identical to Manganese Superoxide Dismutase (MnSOD/SOD2) which has previously been assigned to chromosome 6q25. Localization of 11 clones was determined using PCR and clone-specific primer pairs on a hybrid mapping panel DNA set. Two PCR-localized clones and five additional clones were localized by fluorescence in situ hybridization. Transcripts for five clones were identified by RT-PCR. The generation of chromosome 6-specific hncDNAs from a somatic cell hybrid should aid in the identification of disease-associated genes localized on this chromosome.