SUMMARY Defining appropriate and objective endpoints for animal research can be difficult. Previously we evaluated and implemented a body temperature (BT) of <32 °C as an endpoint for experimental cerebral malaria (ECM) and were interested in a similar endpoint for a model of severe malarial anaemia (SMA). Furthermore, we investigate the potential of a minimally invasive, non-contact infrared thermometer for repeated BT measurement. ECM was induced with Plasmodium berghei ANKA infection in C57Bl/6 mice. SMA was induced with Plasmodium chabaudi AS infection in A/J mice. Our previous published endpoint was applied in ECM and 30 °C was pre-determined as the lowest permitted limit for termination in SMA according to consultation with the Danish Animal Inspectorate. Infrared thermometer was compared with the rectal probe after cervical dislocation, ECM and SMA. Linear regression analysis of rectal versus infrared thermometry: cervical dislocation: Pearson R = 0·99, R 2 = 0·98, slope = 1·01, y-intercept = 0·55; ECM: 0·99, 0·98, 1·06, -2·4; and SMA: 0·98, 0·97, 1·14, -5·6. Implementation of the 30 °C endpoint captured all lethal infections. However, some animals with BT below 30 °C were not deemed clinically moribund. This study supports repeated measurement infrared thermometry. A humane endpoint of 30 °C was sensitive in capturing terminal animals but might overestimate lethality in this SMA model.