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Temperature measurements acquired with an infrared thermometer system and in vivo temperature measurements on the backs of New Zealand rabbits are investigated. Local differences in skin temperature are significant around bony structures and in visceral areas. The results suggest that the location of experimental sites must be considered when interpreting data which use local temperature as an indicator of microvascular phenomena on the skin surface. The techniques are proven valuable for quantifying thermal effects on small fields or skin lesions of experimental animals and can be used noninvasively to measure the onset and transient vascular effects caused by noxious insults, including laser radiation.