Although the evolutionary ecology of melanin pigments and melanin-based coloration has been studied in great details, particularly in birds, little is known about the function of melanin stored inside the body. In the barn owl Tyto alba, in which individuals vary in the degree of reddish pheomelanin-based coloration and in the size of black eumelanic feather spots, we measured the concentration in melanin pigments in seven organs. The eyes had by far the most melanin then the skin, pectoral muscle, heart, liver, trachea, and uropygial gland. The concentration in eumelanin was not necessarily correlated with the concentration in pheomelanin suggesting that their production can be regulated independently from each other. Redder barn owls had more pheomelanin in the skin and uropygial gland than white owls, while owls displaying larger black feather spots had more eumelanin in the skin than small-spotted owls. More data are required to evaluate whether melanin-based traits can evolve as an indirect response to selection exerted on melanin deposition in organs.