To determine baseline variation in blood plasma concentrations of free amino acids and l-lactate, samples were collected at a single time point from nine flocks of different breeds of ewes at a common physiological stage and monthly from one flock of crossbred mule ewes over a 12 month period. Significant differences were detected between time points in the concentrations of all plasma metabolites. With few exceptions prion protein genotype had no significant effect on the plasma metabolite concentrations measured.