Hypothermia is a major cause of mortality in neonatal pigs. Infrared (IR) thermography is a promising non-invasive method to assess thermal status, but has not been evaluated for use on neonatal pigs from birth. The aim of this study was to evaluate the application of IR thermography as a non-invasive tool to estimate body temperature and assess the thermal status in newborn pigs by (1) estimating the relationship between surface temperature and rectal temperature (RT) in neonatal pigs; and (2) estimating the influence of air temperature (AT), birth weight and the time from birth on the relationship between surface temperature and RT. The method was evaluated on the basis of 1695 thermograms and 915 RTs on 91 neonatal pigs born in loose farrowing pens with floor heating at 34°C, and three different ATs (15°C, 20°C and 25°C). Full-body thermograms of the back and the side of the pigs and RT were acquired at 11 sampling times between birth and 48 h after birth. The maximum (IRmax), minimum, average of the full body and ear minimum IR surface temperatures were derived from the thermograms. IRmax had the highest correlation with RT (0.82) and was therefore used in the statistical analysis. The relation of RT by IRmax depended on time at: 0 h (slope: 0.20°C, P<0.001), 0.25 h (slope: 0.42°C, P<0.01), and 0.5 and 1 h after birth (slope: 0.68°C, P<0.001). After the 1st hour (1.5 to 48 h) the relation of RT by IRmax was no longer affected by time (slope: 0.63°C, P<0.001). The agreement between RT and IRmax was improved (P<0.001) after the 1st hour (RT−IRmax 0 to 1 h: 2.02 (1.44)°C; 1.5 to 48 h: 0.95 (0.85)°C). IRmax below 30°C was indicative of piglets having RT<32°C (91.3%). The location of IRmax was identified predominantly at the base of the ears (27/50), other sites in the region of the head (12/50) and the axilla area (8/50). There was a small but significant effect of the angle as IRmax_side–IRmax_back: mean 0.20°C (P<0.001). On the basis of the low difference between IRmax from back and side view thermograms, and the location of IRmax, the angle seems less important and thus the method has the potential to be used without the need for manual restraint of the pigs. On the basis of the results of this study, we propose that IRmax temperature from full-body thermograms has implication as a valid tool to assess the thermal status in neonatal piglets but not as an identical substitute for RT.