The Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic family. The Tat C allele is an interesting marker in the Finno-Ugric context, distributed in all the Finno-Ugric-speaking populations, except for Hungarians. This question arises whether the ancestral Hungarians, who settled in the Carpathian Basin, harbored this polymorphism or not. 100 men from modern Hungary, 97 Szeklers (a Hungarian-speaking population from Transylvania), and 4 archaeologically Hungarian bone samples from the 10(th) century were studied for this polymorphism. Among the modern individuals, only one Szekler carries the Tat C allele, whereas out of the four skeletal remains, two possess the allele. The latter finding, even allowing for the low sample number, appears to indicate a Siberian lineage of the invading Hungarians, which later has largely disappeared. The two modern Hungarian-speaking populations, based on 22 Y-chromosomal binary markers, share similar components described for other Europeans, except for the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection, and high frequency of haplogroup J in both Szeklers and Hungarians. MDS analysis based on haplogroup frequency values, confirms that modern Hungarian and Szekler populations are genetically closely related, and similar to populations from Central Europe and the Balkans.