Preliminary epidemiological data showed a high but varying prevalence of factor V Leiden mutation in various European populations. To analyze population differences statistically and generate reliable evaluation criteria for morbidity estimates, large numbers of unselected probands from different populations have to be tested. A convenient, efficient, reliable and cost efficient method for large-scale screening of factor V Leiden mutation has been developed using capillary blood samples soaked onto filter paper cards for the detection of mutations by heteroduplex analysis. Screening 1,628 alleles of a north-eastern German population by this procedure revealed an allele frequency of 3.56% (carrier rate 7.12%) which is significantly higher than those published for Italy and the Netherlands. Differences in allele frequencies compared to other European populations could statistically not be proved based on the small size of the published samples.