Lee et al. (2007) showed that red clover; with the PPO1 gene silenced (Sullivan and Hatfield 2006), exhibited higher levels of lipolysis than the wild type in the presence of rumen micro-organisms. This questioned the hypothetical mode of action of polyphenol oxidase (PPO) being solely deactivation of the plant enzymes and implied some level of protection of the red clover lipid. It was hypothesised that this may be as a result of protein-phenol complexes, formed by the action of PPO, complexing around lipid micelles and so offering a level of protection. This study investigated whether red clover lipid is protected in the absence of such protein matrixes. At the same time levels of free amino acids were monitored in cultures with the protein matrixes formed to determine whether these offer any form of protection from microbial degradation.