Miscanthus giganteus and Miscanthus goliath are perennial grasses that are native to subtropical and tropical regions of the world. In the UK and Europe, Miscanthus is being extensively trialed as a biofuel. We have recently demonstrated polyphenol oxidase (PPO) and laccase activity in this temperate grass; however, no endogenous substrates have yet been identified. Here we describe studies on the isolation of PPO substrates and PPO and laccase activity from two Miscanthus varieties. The free phenol fraction of Miscanthus leaves and stems were extracted with cold aqueous methanol and extracts were partially purified on a C18 reversed-phase extraction cartridge. Phenols were separated on a HPLC C18 column under a methanol gradient, detected with a photo diode array (PDA) detector and individual peaks were collected for analyses by electrospray ionization-tandem mass spectrometry (ESI-LC-MS/MS). Four caffeoylquinic acids (1-CQA, 3-CQA, 4-CQA and 5-CQA), four feruloylquinic acids (1-FQA, 3-FQA, 4-FQA and 5-FQA) and three coumaroylquinic acids (1-p-CQA, 3-p-CQA and 5-p-CQA) were identified in the leaves and stems of Miscanthus giganteus. Furthermore, free ferulic acid and p-coumaric acid were detected in the stem fraction. In Miscanthus goliath, four caffeoylquinic acids (1-CQA, 3-CQA, 4-CQA and 5-CQA), four feruloylquinic acids (1-FQA, 3-FQA, 4-FQA and 5-FQA), 4-coumaroylquinic acids (1-p-CQA, 3-p-CQA and 4-p-CQA and 5-p-CQA), free caffeic acid and p-coumaric quinic were detected in both leaf and stem extracts. Caffeoylquinic acid diastereoisomers and feruloylquinic acid diastereoisomers were also detected in these fractions. In addition, dicaffeoylquinic acid and dicoumaroylquinic acid and 2-o-caffeoylglucarate were also detected in the leaves.