We have rated eye color on a 3-point scale (1 = blue/grey, 2 = hazel/green, 3 = brown) in 502 twin families and carried out a 5-10 cM genome scan (400-757 markers). We analyzed eye color as a threshold trait and performed multipoint sib pair linkage analysis using variance components analysis in Mx. A lod of 19.2 was found at the marker D15S1002, less than 1 cM from OCA2, which has been previously implicated in eye color variation. We estimate that 74% of variance in eye color liability is due to this QTL and a further 18% due to polygenic effects. However, a large shoulder on this peak suggests that other loci affecting eye color may be telomeric of OCA2 and inflating the QTL estimate. No other peaks reached genome-wide significance, although lods > 2 were seen on 5p and 14q and lods >1 were additionally seen on chromosomes 2, 3, 6, 7, 8, 9, 17 and 18. Most of these secondary peaks were reduced or eliminated when we repeated the scan as a two locus analysis with the 15q linkage included, although this does not necessarily exclude them as false positives. We also estimated the interaction between the 15q QTL and the other marker locus but there was only minor evidence for additive × additive epistasis. Elaborating the analysis to the full two-locus model including non-additive main effects and interactions did not strengthen the evidence for epistasis. We conclude that most variation in eye color in Europeans is due to polymorphism in OCA2 but that there may be modifiers at several other loci.Skin, hair and eye colors are some of the most obvious forms of human diversity (Sunderland, 1956), yet the complexities of the genetic mechanisms underlying the differences of these pigmentation phenotypes within individuals remain largely unknown. It is expected that a relatively small set of major genes contribute to the color variation of these cutaneous tissues within diverse human populations. These pigmentary genes are also expected to be specifically expressed within the melanocyte cell and act to regulate the synthesis, chemical composition, packaging and distribution of the pigment melanin, thus producing the visible differences underlying these traits (Sturm et al., 1998;Sturm et al., 2001).The iris consists of several layers of which the most important for the appearance of eye color are the anterior layer and its underlying stroma (Robins, 1991;Boissy, 1998). In the brown iris there is an abundance of melanocytes and melanosomes in the anterior layer and stroma. In individuals with blue eye color, the anterior layer and stroma contain very little melanin. As light traverses these relatively melanin-free layers, the minute protein particles of the iris scatter the short blue wavelengths to the surface. The blue color is heightened because longer wavelengths (yellow and red) are absorbed by the dark background of the pigmented retinal epithelium which also obscures the reddish hue of the adjacent blood vessels. Other colors such as yellow, green and hazel are due to varying amounts of lipid pigment granules in t...