This paper describes our research on the degradation of ceftiofur and cephapirin at physiological temperatures in kidney extract and in alkaline and acidic solution, conditions that regularly occur during sample preparation. Degradation products were identified using LC-ToF/MS, NMR and microbiological techniques. Additionally kinetics of the degradation processes were studied. A slight instability of cephapirin and desfuroylceftiofur was observed at elevated temperatures. Ceftiofur and cephapirin degraded immediately and completely in an alkaline environment, resulting in inactive degradation products. Ceftiofur and cephapirin also degraded immediately and completely in kidney extract resulting in both formerly reported metabolites as well as not previously reported products. Our research shows that conditions often occurring during the analysis of ceftiofur or cephapirin result in rapid degradation of both compounds. From this it is concluded that underestimation of the determined amounts of ceftiofur and cephapirin is likely to occur. Therefore, a new approach is needed for the analysis of both compounds newly identified degradation products.