Down syndrome (DS) is a major cause of mental retardation and heart disease. Although it is usually caused by the presence of an extra chromosome 21, a subset of the diagnostic features may be caused by the presence of only band q22. Molecular and cytogenetic analysis of a family with 4 DS members has significantly narrowed the chromosomal region responsible for the DS phenotype: congenital heart disease, facial features, and possibly dermatoglyphics. Using high-resolution chromosome banding and in situ hybridization, we found the DS phenotype in the family is caused by a duplication of chromosome 21 material including a region of distal band q22.1 below the limit of cytogenetic resolution, in addition to bands q22.2-q22.3. By quantitative Southern blot analyses of DS members of the family, all random DNA sequences and expressed genes mapping in band q22.1 and proximal are found not to be duplicated. These include cDNA probes for the genes for superoxide dismutase (SOD1) mapping in 21q22.1 and for the amyloid precursor protein (APP) mapping in 21q21.05; D21S46 in 21q11.2-21.05; and D21S47 and SF57 in 21q22.1-q22.3. With one exception, DNA sequences mapping in band q22.3 are duplicated (D21S39, D21SD42, and D21S43). This analysis has now been extended to show that D21S17, previously mapped to band 21q22.3, is not duplicated. In conclusion, the genes SOD1 and APP have been excluded from a necessary role in generating the classical DS features, and the proximal border of the chromosomal region causing DS has been defined.