Infrared thermography is a non-invasive tool shown to be useful in detecting claw abnormalities in cattle at an individual and herd level. This study used the technology to monitor foot temperature and investigate the association with lesion presence over time. A 990 cow dairy herd was enrolled and followed for six months, with data collection fortnightly, lesions were identified by examination of any cow with a mobility score >2, using the 0–3 scale. Two level, multilevel analysis of the association between ambient temperature and foot temperature found that the former was a significant predictor of the latter (coefficient estimate (se)=0.277 (0.02)). Actual foot temperatures were calculated by adjusting for this covariate to allow monitoring over time. Presence of a lesion was also found to be a significant predictor of foot temperature (coefficient estimate (se)=0.623 (0.19)), when added to the model, furthermore some lesion types, claw horn and multiple lesions, were found to be associated with differential foot temperatures. When monitoring lesions over time, the mean adjusted foot temperature was highest at the point of lesion identification. A marked drop in temperature then followed after the lesion was trimmed, with the lowest mean temperature recorded six weeks after treatment, significantly different from the point of lesion identification (P=0.003). This temperature was also lower than the six weeks prior to diagnosis of the lesion, suggesting inflammation was present for at least six weeks prior to the behavioural sign of lameness was seen.