Xanthophylls are a class of bioactive compounds known to play an important role in preventing age-related macular degeneration. Egg yolk is a rich source of highly bioavailable xanthophylls including lutein and zeaxanthin. The effects of domestic cooking methods (boiling, frying, microwaving) on egg yolk xanthophyll content were investigated. A LC-(APCI)-MS/MS method was used to identify and quantify all-E- and Z-isomers of lutein, zeaxanthin, canthaxanthin, and β-apo-8'-carotenoic acid ethyl ester in fresh and cooked egg yolks. Both fresh and cooked yolks showed similar xanthophyll profiles but with higher contents of Z-isomers in cooked samples. All-E-lutein was the most affected, with 22.5%, 16.7%, and 19.3% reductions in boiled, microwaved, and fried yolk extracts, respectively. Total xanthophyll losses ranged from 6% to 18%. The results presented here could be useful in calculating the dietary intake of xanthophylls and also in assessing the xanthophyll profiles and contents of egg-containing products.