The minisatellite locus D1S80, (location: 1p35– p36), GenBank sequence accession # D28507), is a variable number of tandem repeat (VNTR) locus with a 16 base pair repeat size. The sequence of the predominant core repeat region and variants of the D1S80 locus were determined to ascertain whether sequence variation or size variation is the cause of altered migration of some D1S80 alleles. A total of 23 alleles from 14 individuals, previously typed based on the number of repeats (i.e. nominal alleles) for the D1S80 locus, were selected for sequence analysis. The individuals were from African American, Caucasian, and Hispanic databases. From these, 18 different repeat unit sequences were observed and arbitrarily designated A–R. Structural relationships between the alleles became more apparent when the arrays of repeat units were divided into common motifs or super-repeat domains. Six motifs ranging from 3 to 9 repeat units were identified. Several of the alleles included repeat arrays which were too diverse to predict an evolutionary relationship, however, there are two general repeat motif arrays and each has some relationship with either the 18 or the 24 repeat allele. The D1S80 allelic polymorphism is primarily due to variation in the number of repeat units and to sequence variation among repeats, however, it can not be ruled out that some rare alleles may be due to insertions or deletions.