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A comparative analysis of egg yolk proteome of three major poultry species, namely, chicken, duck, and quail, was carried out with two-dimensional (2D) gel electrophoresis patterns and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry. Proteins identified from these three poultry species shared high degrees of sequence and structure homology, which might be related to the bird’s adaptability under different environmental stresses. Few specific proteins were found in this study. Comparative 2D gel electrophoresis patterns of chicken, duck, and quail revealed that some protein-specific regions on gels could be used for authentic identification of poultry eggs. These findings could provide a fundamental understanding of different poultry egg protein profiles and showed us some new sights in egg yolk nutrients related to certain properties and functions.