To investigate the population genetic characteristics and genetic affinity, DNA profiles of three highly polymorphic VNTR (variable number of tandem repeats) loci (DIS7; D7S22 and D12S11) were studied in 405 individuals from three major European populations (English, Spanish and Basques). Like other studies on VNTRs, a large significant heterozygote deficiency was observed in all three populations. This decrease was ascribed to the limitation, coalescence and non-detectibility of alleles associated with the RFLP (restriction fragment length polymorphism) technique, through which the VNTR loci are genotyped. When the non-detectable alleles were taken into consideration, analyses of fragment sizes at these loci within each sample, as well as their fixed binned analyses, reveal that the assumptions of independence of allelelic occurrences within and between loci are valid for this European data. By comparing genetic variation at three VNTR loci with 17 blood groups, proteins and HLA loci in three well defined European populations, it is shown that the pattern of differentiation at these sets of loci are in general parallel especially for the hypervariable loci HLA and VNTR. Fixed-bin allele frequencies, therefore, are the best descriptions of such a database both for population genetic and forensic calculation studies. The Basques, with regard to VNTR loci, do not show any reduced genetic variability compared to other two European populations (English and Spanish).