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Y Chromosome Single Nucleotide Polymorphisms Typing by SNaPshot MINISEQUENCING Analysis of Y chromosome haplogroups, defined by single nucleotide polymorphisms (SNPs), is now a standard approach for study of the origin of human populations and measurement of the variability among them. It is also a new forensic tool, because it may allow determination of the origin of any male sample of interest. We have used a strategy for rapid, simple and inexpensive Y chromosome SNP typing of 343 male DNA samples, of which 211 were Macedonians, 111 Albanians and 21 Roma, Serbs or Turks. Using multiplex polymerase chain reaction (mPCR) and a SNaPshot multiplex kit for single nucleotide extension reaction, 28 markers were grouped into five multiplexes. Twenty different Y haplogroups were found in these samples. The most common Y haplogroups in Macedonians were I2a-P37b (27.5%), E1b1b1a-M78 (15.6%), R1a1-SRY1532 (14.2%) and R1b1-P25 (11.4%). In the Albanians E1b1b1a-M78 accounted for 28.8%, R1b1-P25 for 18.0%, J2b2-M241 for 13.5% and R1a1-SRY1532 for 12.6%. We conclude that five haplogroups (E1b1b1a-M78, I2a-P37b, J2b2-M241, R1a1-SRY1532 and R1b1-P25) comprised 72.6% of the Y chromosomes, this being characteristic of the typical European Y chromosome gene pool.