Qualitative information on the sequence composition of the allele and locus structure of the X-STRs DXS8378, DXS9898, DXS6789, GATA31E08, and GATA172D05 was generated in this study. Sequence data were obtained from chimpanzees (Pan troglodytes) and diverse human population groups including Africans, Caucasians, Asians, African-Americans, and Hispanics. Results revealed DXS8378 as the most stable locus. On the other hand, DXS9898 and GATA172D05 showed unstable regions identified through chimpanzee-human sequence comparison. At DXS6789, intra-allelic variation was found in all human populations, i.e., alleles with same fragment sizes showed structural differences only detected by sequencing. At the GATA31E08 locus, a previously unreported variation between humans and chimpanzees was identified in an adjacent region upstream from the repeat. This resulted in the addition of two repeat units and the proposal of a new allele nomenclature at this locus. Also, the sequence analyses did not detect ethnic differences between the studied population samples that would justify the use of these markers to help identify ethnic origin in an anthropological context.