We used implanted miniature data loggers to measure brain (in or near the hypothalamus) and carotid arterial blood temperatures at 5 min intervals in six free-ranging ostriches Struthio camelus in their natural habitat, for a period of up to 14 days. Carotid blood temperature exhibited a large amplitude (3.0–4.6°C) circadian rhythm, and was positively correlated with air temperature. During the day, brain temperature exceeded carotid blood temperature by approx. 0.4°C, but there were episodes when brain temperature was lowered below blood temperature. Selective brain cooling, however, was not present in all ostriches, and was not tightly coupled to the prevailing body temperature. Brain temperature was maintained within narrow daily limits of approx. 2°C, and varied significantly less than blood temperature at short time scales of 5 to 20 min. At night, brain temperature exceeded blood temperature by as much as 3°C. We attribute the elevated brain temperatures to warming of cerebral arterial blood, by reduced heat exchange in the ophthalmic rete or possibly heat gain from cranial structures, before supplying the hypothalamus. Further studies are necessary to elucidate the significance of such variations in brain temperature and the importance of selective brain cooling in free-living birds.