The most comprehensive study of Y-chromosomal diversity in Europe thus far is Rosser et al., . The human Y chromosome is passed on from father to son. One can thus study one half of a population's ancestry (along the paternal line) by studying the Y-chromosome. Greek Y-chromosomes belong to haplogroups HG1, HG2, HG3, HG9, HG21 and HG26. None of the 35 Greek Y chromosomes are of non-Caucasoid origin.
A second Y-chromosome study including Greeks have also shown similar results. Helgason et al.,  reports one HG16 sequence of North Eurasian provenance in a sample of 42 Greeks (at least 97.6% Caucasoid). To put this in perspective, eight HG16 chromosomes occur in 110 Swedes (at least 92.7% Caucasoid) and three HG16 sequences in 112 Norwegians (at least 97.3% Caucasoid) were also found. HG16 is shared by many populations ranging from Europe to Mongolia. Its origin has been placed by  in the Eastern range of its current geographical distribution.
A third Y-chromosome study, by Malaspina et al.,  which included a sample of 28 continental and 83 Cretan Greeks (total sample size of 111) found no evidence of the presence of non-Caucasoid Y chromosomes in Greeks.
A fourth Y-chromosome study, by Semino et al.,  included 76 Greeks and 20 Macedonian Greeks. One Eu6 lineage, corresponding to HG10/HG36  is probably of East Asian origin. One Eu17 lineage corresponds to HG 28 which is frequent in Central Asia and the Indian subcontinent . In total, admixture of 2.1% is detected (if we label HG 28 as non-Caucasoid).
A fifth Y-chromosome study, by Weale et al.,  included 132 Greek students from Athens. The same haplogroups found in  were detected in this study. No non-Caucasoid chromosomes were found.
The most recent and comprehensive study of Greek Y-chromosomes, by Di Giacomo et al.,  included 154 individuals from continental Greece and 212 from Crete, Lesvos and Chios. In total, Greeks from thirteen separate locations were examined, thus giving the most complete picture of variation so far. A single haplogroup A chromosome was found (in Lesvos) which is usually found in Africa. The remainder belonged to haplogroups found in Caucasoid populations. The breakup (in percent) of the haplogroups observed) based on the set of markers typed is as follows.
|P*(xR1a)||R1a||DE||G2||I-M170||J2(DYS413= 18)||J2*(xDYS413= 18)||J*(xJ2)||A||Y*(xA,DE,G2,I,J,P)|
A newer study by Semino et al.  has studied two samples of Greeks of size 84 and 59 (Macedonian Greeks). The focus was on two specific haplogroups E and J which are frequent in the Mediterranean region and can be used to detect population movements between Europe, Africa and the Near East. 2.4% of Greeks belong in haplogroup E-M123 and 21.4% in E-M78. Clades of E prevalent in Northern or Sub-Saharan Africa were not found. According to Cruciani et al.  most Greeks and other Balkan people belong to a specific cluster a within haplogroup E-M78 that is found in lower frequencies outside the Balkans and marks migrations from the Balkan area. E-M123 and its daughter haplogroup E-M34 originated in the Near East in prehistoric times. As for haplogroup J, most Greeks (22.8% Greeks/14.3% Macedonian Greeks) belong to J-M172 and its subclades which is associated with Neolithic population movements. Only 1.8%/2.2% of Macedonian Greeks/Greeks belonged to haplogroup J-M267 which could potentially (althought not certainly) reflect more recent Near Eastern admixture.
Bosch et al.  studied Y chromosome variation in the Balkans, including a sample of 41 Greeks. Greeks belonged to the major Caucasoid haplogroups. The identity of the K*(xP) chromosomes is not clear, but they could belong to the minor Caucasoid haplogroups K2 and L which have been previously observed in Greeks, or to other K-related lineages.
Firasat et al.  tested 77 Greeks as part of a study of the purported Greek origins of certain ethnic groups of Pakistan. The breakdown of the observed haplogroups is given in the table below. One haplogroup H2 was observed, which is more typical of South Asian populations.
Martinez et al.  has studied a sample of 168 Greek men from Lasithi and Heraklion in Crete. No Sub-Saharan African influence was detected, and 2 Q chromosomes, which could conceivably be indicative of Asian influence were detected. The exact origin of these is uncertain, since no downstream markers were typed. The Y chromosome haplogroups detected in this sample are listed below (click to magnify).
Battaglia et al.  have studied a sample of 92 Greek men from Athens and 57 Macedonian Greeks. With the exception of a single haplogroup C chromosome, all other men belonged to typical Caucasoid Y-chromosomes. The occurrence of haplogroup E-M81 in four men, and J1 in three men, may reflect North African (2.7%) or Near Eastern (2%) input into the Greek population. The resuts of this study are listed below:
Thus, at present, in a total of nine studies, in which 1,724 Greek males were tested, one HG16, one HG28, one HG10/HG36, one H2, one haplogroup A, two haplogroup Q, and one haplogroup C chromosomes have been found, for a total of 0.46% possible non-Caucasoid contribution to the modern Greek male gene pool. Additionally, the latest studies [9, 10, 18] with a more refined version of the Y chromosome phylogeny indicate that influences from the Near East and North Africa in historical times are unlikely (perhaps in the order of ~2%). Additionally, Y chromosome haplogroup R1a which is very frequent in Slavic populations (>50%) is found in only around ~10% of Greeks, and is also found at comparable frequencies further East (10.8% in Iraq; Al-Zahery et al. ) indicating that its presence in Greece need not be associated with medieval intrusions by Slavic speakers. The emerging picture of Y chromosome variation in Greece indicates genetic continuity, with slight influences from neighboring Caucasoid regions and virtually no influence from non-Caucasoids.
Future studies with larger samples and more detailed founder analyses will allow us to obtain a better pictures of Y-chromosome variation in Greece, Europe and the world at large. At present, it appears that modern Europeans share many of the haplogroups, while there is also geographic structure in the distribution. With the exception of the Northeast corner of Europe, all other European populations have very small traces of extra-Caucasoid genetic input(a).
- Rosser et al. (2000) European Y-Chromosome Diversity. Am J Hum Genet 67:1526-1543
- Helgason et al. (2000) Ancestry of Icelandic Y Chromosomes. Am J Hum Genet 67:697-717
- Malaspina et al. (2000) Patterns of male-specific inter-population divergence in Europe, West Asia and North Africa. Ann Hum Genet 64:395-412
- Semino et al. (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective
- Zerjal et al. (2002) Y-Chromosomal Insights into Central Asia. Am J Hum Genet 71:466-482
- Qamar et al. (2002) Y-Chromosomal DNA Variation in Pakistan. Am J Hum Genet 70:1107-1124
- Zerjal et al. (1997) Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am J Hum Genet 60:11741183
- Weale et al. (2001) Armenian Y chromosome haplotypes reveal strong regional structure within a single ethno-national group. Hum Genet 109: 659-674
- Di Giacomo et al. (2003) Clinal Patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects. Mol Phyl Evol 28:387-395
- Semino et al. (2004) Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area. Am J Hum Genet (to appear)
- Cruciani et al. (2004) Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out Of Africa. Am J Hum Genet (to appear)
- Al-Zahery et al. (2003) Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations. Mol Phyl Evol 28:458-472
- Flores et al. (2005) Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan. J Hum Genet. (to appear)
- Bosch et al. (2006) Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns. Ann Hum Genet. (to appear)
- Firasat et al. (2006) Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan. Eur J Hum Genet. (to appear)
- Laisel Martinez et al. (2007) Paleolithic Y-haplogroup heritage predominates in a Cretan highland plateau, European Journal of Human Genetics
- King et al. (2008) Differential Y-chromosome Anatolian Influences on the Greek and Cretan Neolithic, Annals of Human Genetics 72,205–214
- Battaglia et al. (2009) Y-chromosomal evidence of the cultural diffusion of agriculture in southeast Europe, European Journal of Human Genetics (in press)
(a) This author does not maintain that there is anything wrong in principio with non-Caucasoid influences.