The Hungarian surname Hajdú is from hajtó or ‘drover’. Drovers traveled armed, and sometimes ended up as highwaymen, mercenaries, or retainers in the service of local landowners. Hajdú acquired all these meanings, but the surname is chiefly associated with the settlement of hundreds of mercenaries in eastern Hungary by Prince István Bocskai as a reward for their support.  

In1604-1606, István Bocskai, Lord of Bihar,led an insurrection against the Habsburg Emperor,whose army had recently occupied Transylvania and begun a reign of terror. The bulk of Bocskai's army was composed of serfs who had either fled from the war and the Habsburg drive toward Catholic conversion, or been discharged from the Imperial Army. These peasants were known as the hajduk, a term associated in the Hungarian language with the cattle drovers of the Great Plains. These mainly Calvinist hajdú were considered the reserve units of the imperial forces,but –  because they were never paid regularly – lived rather miserably on the margins of society. It was with the arms of the hajdú that Bocskai defended himself against the imperial forces stationed in the region, and he owed it primarily to them that, in spite of two defeats in battle, by the end of the year he was the effective master of all of northern Hungary, .elected first prince of Transylvania, and then of Hungary.

Asa reward for their service, Bocskai emancipated the hajduk from the jurisdiction of their lords, granted them land, and guaranteed them rights to own property and to personal freedom. The emancipated hajduk constituted a new "warrior estate" within Hungarian feudal society. Many of the settlements created at this time still bear the prefix Hajdú such as Hajdúbagos, Hajdúböszörmény, Hajdúdorog, Hajdúhadház,Hajdúnánás, Hajdúsámson, Hajdúszoboszló, Hajdúszovát, Hajdúvid etc., and the whole area is called Hajdúság (Land of the Hajduk).

The name is also borne by Hungarian Jews, generally as an ornamental adoption of the Hungarian name.

This surname project seeks to identify the descendants of the Hajdús who originally received a warlike coat of arms from Prince István Bocskai in the early 15^th Century, one version of which may be found at/ :

http://en.wikipedia.org/wiki/File:Hajdu_coatofarms.jpg

Given this history, however, it cannot be assumed that all of the emancipated Hajdúshad similar Y chromosomes at the time they were freed. It will be interesting to discover how many different lineages end up claiming this family history.