The production and removal of anaerobiotic compounds, principally ethanol from flooded tree roots was examined in lodgepole pine (Pinus contorta) from known provenances. Contrary to earlier suggestions, the gaseous pathway, with ethanol exiting from the tree through the lenticels, removes only a very small proportion (less than 0.2%) of the ethanol generated in the flooded roots. The transpiration stream provides the major route for ethanol transport from the roots. Although the lenticels do not contribute significantly to the removal of ethanol from tree roots, analysis of the gas exiting from them provides a sensitive indicator of the existence of oxygen within roots. Within the xylem sap and root tissue, changes in ethanol, amino acid (alanine, alpha amino butyrate and glutamine) and organic acid (malate and shikimate) composition under flooded conditions were analysed and discussed. For example during flooding glutamine (the major constituent amino acid) was shown to decrease, and alanine and alpha amino butyrate to increase. From the data obtained it was concluded that the health and the metabolism of the root tissue during flooding can be diagnosed by examination of the xylem sap.