Eye colour is a prominent visible trait in Europeans and is of significance in forensic genetics. Eye colour is most commonly categorised in a three-category system comprising brown, intermediate, and blue eye colours. However, the general perception of eye colour categories has not been explored. Here, we categorised eye colour based on the subjective evaluation of 442 digital close-up photos of eyes assessed by 30 Danish volunteers. The participants were asked to categorise each eye in a three-category (brown, intermediate, blue) and a two-category (brown, blue) system. We found that the two-category system corresponded best with the perception of eye colour. Disagreements in the eye colour categorisation by at least 10% of the participants were observed for 33% of the eye pictures using the three-category system. In comparison, only 10% of the pictures were categorised differently by at least 10% of participants when using the two-category system. The genetic basis for distinction between blue and brown eye colour primarily depends on a single SNP, rs12913832. Likelihood ratios based on the genotype of rs12913832 and the two-category system were: LR = P(rs12913832:GG|brown)/P(rs12913832:GG|blue) = 0.1, LR = P(rs12913832:AA|brown)/P(rs12913832:AA|blue) = 54, and LR = P(rs12913832:GA|brown)/P(rs12913832:GA|blue) = 19. This SNP is included in the Precision ID Ancestry panel used for ancestry inference, which enables genetic ancestry profiles to be accompanied by prediction of blue or brown eye colour.