DNA polymorphisms can be used to place loci and phenotypes on the linkage maps of human chromosomes. In an effort to localize genes on the linkage map of human chromosome 21 better, we examined their 3' untranslated (3'UT) regions for the presence of polymorphisms. We amplified the 3'UT region of 17 genes of chromosome 21 by the polymerase chain reaction and subjected the product to single-stranded conformation analysis (SSCA). We have found eight polymorphisms in the 3'UT region of genes. The total area examined was 8144 nucleotides and therefore the variability detected by this method was 1 in 1018 nucleotides. This is not different from the estimated variability of DNA sequences based on restriction analysis. Sequence analysis revealed that all polymorphisms found are due to single nucleotide substitutions. Additional polymorphisms were identified in the last intron of BCEI gene and in the 3'-flanking region of the S100B gene. We conclude that the 3'UT region of genes is a relatively rich source of polymorphisms and that SSCA is an effective method of detecting the normal sequence variation in the human genome.