A HPLC method with improved sensitivity for the determination of ochratoxins (OT) A, B and α in plasma and milk was developed. Plasma analysis involved a simple liquid–liquid extraction with chloroform; while for milk, an additional immunoaffinity clean-up step was necessary. The method showed a good linearity (r 2 >0.999). The limit of quantification (LOQ) of OTA was 5 and 200ng/l for milk and plasma, respectively. Average recovery was 89% in both matrices, except for OTα in milk that was only 18% due to poor immunoaffinity binding. OT remained stable in −20°C stored samples; OTA concentration in plasma and milk did not change after 8 and 18 months of storage, respectively. The developed method has been applied to contaminated plasma and milk samples obtained from dairy ewes fed with ochratoxin-contaminated feed.