Normal-phase (NP) liquid chromatography is one of the most effective methods for separating isomers with sensitive structural features, including xanthophyll isomers. In this work, reverse-phase (RP) and NP liquid chromatography (LC), with silica gel and diol phase, respectively, were evaluated for the separation of xanthophyll isomers. The results showed that RP LC with monomeric C18 phase not only poorly separate all xanthophyll isomers in egg yolk but also requires additional sample preparation to eliminate triacylglycerols in egg yolk. The diol phase of NP-LC provided the highest efficiency for separating lutein, zeaxanthin, and their cis-isomers with isocratic separation using mobile phases consisting of n-hexane and polar modifiers (such as acetone, methyl tert-butyl ether, or ethyl acetate). To determine the xanthophyll content, peak areas from LC and total absorbance from spectrophotometry measurements were used. The approach was applied to analyze the xanthophylls of nine commercial egg samples. The results revealed that five out of nine analyzed samples contained a high level of canthaxanthin, which contributes to color enhancement but not to prevent age-related macular degeneration. Together, it shows that NP LC with diol phase combined with spectrophotometry is a powerful tool to monitor xanthophylls in eggs.