Variation in human hair and skin color is the most striking visible aspect of human genetic variation. The only gene known to exert an effect on pigmentary within the normal population is the melanocortin-1 receptor (MC1R). Previous studies have used a Mendelian framework to relate MC1R genotype to phenotype, by measuring pigmentary status using categorical scales. Such approaches are inadequate. We report results using direct measures of hair color using objective colorimetric dimensions and HPLC determined hair melanins. We have linked MC1R genotype with chemical measures of melanin quantity and type and objective phenotype measures of color. MC1R genotype was predictive of hair melanin expressed as the ratio of the loge of eumelanin to pheomelanin ratio, with a dosage effect evident: MC1R homozygote mean, 1.46; heterozygote, 4.44; and wild type, 5.81 (p<0.001). Approximately 67% of the variance in this model could be accounted for in terms of MC1R genotype. There was also a relation between MC1R status and hair color, most prominently for the b* axis (p<0.001), but also for the a* and L* scales (L*a*b*, CIE). We show for one of the most polymorphic human traits that it is possible to demonstrate meaningful relations between various physical characteristics: DNA sequence diversity, hair-wavelength-specific reflectance patterns, and chemical melanin assays.