In many indigenous minority populations, and among migrants from Asian and African populations now resident in western Europe, North America and Australia, there is a strong tradition of endogamy and a preference for consanguineous unions. These marriage practices can result in F(ST) values greatly in excess of the maximum value (0.01) currently recommended for forensic DNA purposes under guidelines established by the National Research Council (NRC) of the USA. To examine the possible extent of deviation from this accepted norm, three co-resident Pakistani communities were studied using 10 autosomal dinucleotide markers and six tetranucleotide markers on the Y-chromosome. The mean population subdivision coefficient (FST) value was 0.13 for the autosomal loci, and Y-chromosome loci exhibited even stronger differentiation with unique alleles identified in all three communities. The data indicate that even when sub-populations are virtually indistinguishable in terms of anthropology, geography, ethnicity or culture, they may still exhibit major genetic differentiation. Where significant population stratification is known to exist, more detailed genetic databases should be developed for forensic DNA purposes, based on reference data from each of the appropriate sub-populations and not on random or combined samples.