Application of a method for the fine structure analysis of unbalanced chromosomal rearrangements using quantitative Southern blot analysis has established that an individual of normal intelligence and largely normal appearance has a significant interstitial deletion of chromosome 21. Using high resolution cytogenetic analysis and molecular analysis with five single copy DNA sequences unique to chromosome 21 and a probe for human SOD1 (CuZn, superoxide dismutase), we find that the deletion extends to the border of bands 21q11.1-11.2. and extends to the border of bands 21q21.2-q21.3. The latter border is established molecularly by the presence of two copies of SOD1, previously mapped to band 21q22.1, and of four single copy sequences known to be located distal to this region. The presence of SOD1 was confirmed by enzyme dosage analysis. These findings demonstrate that deletion of close to 20,000 kb of autosomal material is compatible with normal intelligence. Further, they suggest that chromosome 21 may include a large region of relative developmental neutrality whose molecular basis may now be investigated. Because of the limits of even high resolution cytogenetic analysis, fine structure molecular analyses of this type will be necessary to reliably detect and define similar small chromosomal deletions or insertions. The molecular definition of such aneuploidy provides the basis for increasing the resolution of the human physical genetic map.