Y-chromosomal variation of Central European populations and the possible appearance of genetic isolates in these populations are of increasing interest to forensic and human population geneticists. Y-chromosomal data for the population of the Czech Republic is still fractional. Kracmarova et al published a short report on paleolithic and neolithic Y chromosomal haplogroups in the Czech population (1) and Luca et al performed a refined study of the same data (2). Zastera et al published a major study on Czech Y-chromosomal data (3). Other authors have also reported on Czech Y-chromosomal variation, usually with other population data from Europe (4-7). A recent study compared Czechs with other West Slavic populations (8). In this range of reports regarding, genetic variation of possible or confirmed genetic isolates within Central European populations is virtually absent. Here we present the intra-population diversity of such an isolated population, the Moravian Valachs. So far, a limited number of studies that illustrate the variety of Y-chromosomal polymorphisms in the countries and populations supposedly connected or similar to the Moravian Valachs – the supposed isolate – have been published. Rebala et al (9) focused on the Slavic population from Eastern and Central Europe. As historical sources suggest, immigration from Slavic populations was one of the major sources for the emergence of the Valach population of the Czech Republic, therefore the study of Rebala et al (9) is certainly of great interest to us, as well as other studies on southern European Slavic populations (10). Bosch et al (11) analyzed paternal (and maternal) lineages of the Aromuns and other surrounding Balkan populations, thus offering excellent material for their comparison with the Valachs. They clearly documented the differences between Aromuns (ie, isolated populations) and the major populations that surround them, not only in haplogroup and haplotype lineages, but also in intra-population genetic variability. The Valachs (or Wallachs/Vlachs as they are sometimes called) are one of the most distinct ethnographic and cultural subpopulations of Central Europe. Today, they can be found not only in the Czech Republic – in its eastern border mountain ranges and highlands (Beskydy in Moravia) – but also in south-southeast Poland and several parts of Slovakia (far western, northern, and central region). Originally, this group spread from the Maramures region of Romania, roughly following the Carpathian Mountain range. The arrival of the Valachs to the area of today’s Czech Republic took place at the very end of the 15th or beginning of the 16th century (12). The migration was not spontaneous, but rather encouraged and subsidized by the local nobility, and it lasted at least until the end of the 18th century, with immigrants supposedly coming not only from Romania, but also from Ukraine, Poland, and Slovakia (13). Until the beginning of the 20th century, the Moravian Valachs’ way of life was similar to other Romanian ethnic groups in the Balkans, especially the Aromuns (seasonal mountain sheep herding, production of cheese, wool, and leather products). An admixture of the newly-arrived Valachs with autochthonous (Slavic and German) Moravian population also began soon after the arrival of the first immigrants – so we can assume a steady genetic and cultural flow between these two populations. Nonetheless, the core of the Valach settlement was located in a previously uninhabited high altitude region, neighboring with the indigenous population from lowlands. The result of the admixture process was a complete merging of both populations, and the disappearance of any distinction between “new” Valachs and indigenous Moravians during the 18th century, and the creation of one ethnogeographic region with all its properties and people – the Moravian Valachs. Demographic data (13,14) show only a small increase in the Valach population during the 17-18th century. In combination with population depression during and after the Thirty Years' War (1618-1648), the conditions in the Valach population favored inbreeding, an effect reinforced by isolation-by-distance from the surrounding populations. To investigate how severe this isolation effect was on Y chromosomal polymorphisms in the Moravian Valachs and whether it is still detectable in modern Valach population is the main aim of our study. Another topic of interest was how the intra-population variability and the sampling bias can affect forensic and population analyses performed on these data.