A rare variant of 6q11+ heteromorphism was found in a fetus and the mother during amniocentesis. The G- and Q-banding and DA/DAPI stain were negative. The C-banding was positive and the C-banded segment was 3-fold longer in the variant than in its homologue. Neither of the C-banded regions of chromosomes 6 decondensed when exposed to distamycin A or 5-azacytidine. A DNA replication study indicated that the C-banded variant was late replicating. The lateral asymmetry observed in the 6q11 variant after one replication cycle in 5-bromodeoxyuridine may result from an unequal interstrand distribution of thymidine in the repetitive DNA. Fluorescent in situ hybridization using a chromosome-6-specific alpha-satellite probe (D6Z1) demonstrated hybridization signals on the centromere of chromosome 6. The 6q11 variant showed a signal which was 3-fold larger than its homologue. These results indicate that the 6q11 variant is an amplification of a chromosome-6-specific alpha repeat, and the size of the hybridization signal correlates with the size of the laterally asymmetric and C-banded region.