Egg yolks are colored by xanthophylls, a yellow-orange pigment in green plants, yellow corn, and bugs. Yolk color is influenced by feed, exercise, and the lifestyle of the chicken. Yolk color can be influenced by feed alone. In fact, a chicken running around in a yard, eating whatever it finds, is going to have varying yolk color intensity, depending on what is in season. Alfalfa creates a very light yellow yolk, whereas yellow corn can give a deeper yellow. More-intense-colored yolks are the result of feed with a heavy dosing of annatto or ample greens such as clover or kale; rye pasture; weeds such as mustard, pennycress, and shepherd’s purse; or feed that is high in beta-carotene vegetables such as carrots and beets. A quantity of red fruits can intensify the red-orange color of the yolk.
Exercise, pecking order, and bug eating contribute to the natural deep orange and/or red tones of a naturally colored yolk.
In the “modern world” we mess with mother nature.
Poultry raisers have long discussed influencing yolk color with various feed combinations to please their consumers. In 1919 a popular paper entitled “The influence of specific feeds and certain pigments on the color of the egg yolk and body fat of fowls,” by Leroy S. Palmer and Harry L. Kempster, was widely read. What the authors found was that “yellow corn is the best winter food for keeping up the coloring of adipose tissue during fattening” and that it was also what kept the egg yolks a nice sunny yellow color. Not too dark, not too light. People liked to purchase dressed chickens with a deep yellow skin color, and corn filled the bill. Corn, along with annatto (a derivative of the achiote tree, of tropical regions of the Americas, used in food dyes), is used heavily—to this day—in chicken feed to give a faux “healthy” yellow glow that normally could be found only in chickens raised in sunshiny fields.
A side note: Annatto has been linked with many cases of food-related allergies and is the only natural food coloring believed to cause as many allergic-type reactions as artificial food coloring. However, because it is not one of the “Big Eight” allergens (cow’s milk, eggs, peanuts, tree nuts, fish, shellfish, soy, and wheat) responsible for more than 90 percent of allergic reactions to food, its use is not regulated nor is a consumer able to avoid it easily (it’s rarely listed in labeling as anything other than “natural coloring”). Many people who consider themselves allergic to chicken eggs may, in fact, be allergic to the annatto feed additives.
Artificial egg coloring is still a very hot topic in poultry farming. Articles appear frequently in trade and scientific journals regarding the use of artificial and natural coloring agents in feed to intensify the yolk color of eggs and the skin color of chickens. One such article, “Formulation of Annatto Feed Concentrate for Layers and the Evaluation of Egg Yolk Color Preference of Consumers,” in the Journal of Food Biochemistry (January 13, 2010), lays out the trickery that is rampant in the poultry industry:
Visual appearance, especially color, is one of the most important characteristics of foods and determines the acceptance or rejection of the product by the consumer. This statement is also true for poultry products, in which the color of skin, meat and egg yolk plays a fundamental role to some ethnic and regional consumers (Chichester, 1981; Hencken, 1992; Williams, 1992; Macdougall, 1994). The preference for well-pigmented poultry products is still evident in some markets, and thus, poultry producers add colorants to broiler and layer diets as a means of improving the attractiveness of these products (Klaui and Bauernfeind 1981; Hencken 1992; Liufa et al., 1997).
The interesting thing about the authors’ analysis is their assertion that the average consumer in the United States prefers a yolk that is a lighter yellow than what European consumers favor. This is presumably because those consumers have never eaten an egg from a chicken that pecks, scratches, chases bugs, and eats greens and weeds in a natural setting. The flavor and quality of eggs from a backyard chicken are vastly superior to what you get with commercially laid eggs.
 I. Ofosu, E. Appiah-Nkansah, L. Owusu, F. Apea-Bah, I. Oduro, I., and W. Ellis, “Formulation Of Annatto Feed Concentrate for Layers and the Evaluation of Egg Yolk Color Preference of Consumers,” 2010. Journal of Food Biochemistry, 34: 66–77. doi: 10.1111/j.1745-4514.2009.00264.x
 The Dairy Chemistry Laboratory and Department of Poultry Husbandry, University of Missouri, Columbia)
i am terribly allergic to annatto and believe i am having issues due to egg yolks from the hen feed. have you been able to identify which brands do this? i am running into issues with the companies claiming that the feed is proprietary, and will not disclose it.