Thermogenesis mediated by brown adipose tissue (BAT) and brown-like fat plays an important role in regulating metabolic homeostasis in mammals. Accurate measurement of metabolic responses to brown fat activation, including heat generation and increased energy expenditure is essential for characterizing thermogenic phenotypes in preclinical studies. Here, we describe two methods for assessing thermogenic phenotypes in mice under non-basal states. First, we describe a protocol for measuring body temperature in cold-treated mice using implantable temperature transponders, which allow for continuous monitoring of body temperature. Second, we describe a method for using indirect calorimetry to measure β3-adrenergic agonist-stimulated changes in oxygen consumption, a proxy for thermogenic fat activation.