Recently, we reported measurements of heterochromatic flicker photometry (HFP) in 22 young observers, with stimuli that (nominally) modulated only L- and M-cones and were kept at (approximately) a constant multiple of detection threshold. These equiluminance settings were represented as the angle in the (L, M) cone contrast plane, with the greenish peak of the flicker in quadrant II and the reddish peak in quadrant IV; equiluminance settings were reported as the greenish angle. The mean equiluminance angle was 116.3° (an M:L cone contrast ratio of -2 at equiluminance), but individual differences in the settings were substantial, with the variation across individuals almost five times larger than the within-subject precision in the settings. In the present study we sought to determine the degree to which we could account for our observers' HFP settings by plausible variations in the macular pigment optical density (MPOD), the lens pigment optical density (LPOD), the cone photopigment optical densities (PPOD), and serine/alanine polymorphism in L-cone opsin (λmax shift). Most of the range of our measured equiluminance angles could be accounted for by these factors, although the largest two angles (smallest |ΔM/M: ΔL/L| ratio at equiluminance) could not. Individual differences in HFP have sometimes been taken to indicate variations in the ratio of L:M cone number; our results suggest that most of the individual differences in HFP might be equally well ascribed to physiological factors other than cone number. Simple linear models allow predictions of equiluminance angle, cone adapting level, and artifactual S-cone contrast from the values of the four factors considered here.