A pressure cuff was applied to the legs of two human volunteers in order to stop any blood supply for a period of about 30 min. The affected muscle was monitored using proton magnetic resonance imaging (MRI), phosphorus magnetic resonance spectroscopy (MRS) and near infrared (NIR) spectroscopy before, during and after this procedure. The internal temperature of the tissue was also measured. The phase of water protons in muscle showed changes that were not accounted for by the measured temperature, but which correlated with the large increase in deoxyhaemoglobin and deoxymyoglobin observed with NIR as well as the decrease in PCr and increase in Pi observed with MRS. Little or no change was found in proton density or T2*. These results show that in vivo measurements of temperature using the chemical shift method may be confounded by changes in tissue oxygenation. They also show that T2* is an insensitive measure of changes in tissue oxygenation.