Polyacrylamide gel electrophoresis (PAGE) is performed routinely in research and diagnostics. The lack of internal standards, however, has been very disadvantageous for PAGE methodologies in comparison to alternative separation techniques like chromatography. Chapter one discusses how comparative fluorescence gel electrophoresis (CoFGE) has the potential to change this situation. Chapter Two focuses on elucidating the properties of polyacrylamide gel matrixes, discussing the essential principles of discontinuous PAGE in technology, and summarising the discontinuous buffer systems employed for the discontinuous PAGE in alkaline, neutral and acidic circumstances. Chapter Three discusses the need for the establishment of typical physiologic protein pattern for various avian patients. Chapter Four discusses constant field gel electrophoresis, a sensitive, rapid, economical and perspective method for detecting DNA double strand breaks and rejoining with high resolution.