Rattlesnakes and pit vipers in the subfamily Crotalinae have a pair of facial pits—sense organs on the head lying below and in front of the eyes that function as highly sensitive thermoreceptors. True boas in the family Boidae also have pits, though they are slightly different in structure from those of the crotalinids. The pit organs act as directional distance receptors and make it possible for the reptile to strike at warm prey. Each pit is a cavity about 1–5 mm (0.04–0.2 inches) deep, equally as wide at the bottom, and narrowing toward the opening at the surface of the head. Inside and separated from the bottom by a narrow air space is a densely innervated membrane of about 15 μm thickness stretching between the walls of the pit. A direct connection between the air space beneath the membrane and the open air maintains equal pressure on both sides of the membrane. Warm-sensitive receptors distributed over the membrane consist of treelike structures of bare (unmyelinated) nerve fibre endings. Radiation (heat energy) reaches the membrane from an external source through the narrow opening of the pit, permitting the snake not only to detect heat but also to localize coarsely the position of the stimulus. The fields of direction (cones of reception) from which each pit can receive radiation from the environment extend to the front and sides of the head, with a narrow zone of overlap in the middle.

Under resting conditions, there is an irregular, steady discharge of nerve impulses from the pit organ. Infrared energy calculated to produce a change of as little as 0.003 °C (0.005 °F) at the nerve endings elicits a significant dynamic increase in impulse frequency; cooling produces an inhibition of the resting discharge. In contrast to the warmth receptors in mammals, the reptile’s pit receptors are practically insensitive to steady temperatures, despite their high sensitivity to rate of thermal change. The distinctive consequence in the snake’s adaptive behaviour is that gradual variations in air temperature tend to occur without detection; only the more rapid changes in radiation are discriminated. Sensitivity to rapid temperature changes is enhanced by the very limited heat capacity of the thin receptive membrane. When an animal that is 10 °C (18 °F) warmer than the environmental background appears for half a second at a distance of 40 cm (16 inches) in front of the snake, the heat energy radiated is enough to elevate the frequency of receptor discharge in the pit organ. Indeed, behavioral experiments show that under these conditions the snake is able to discover warm prey through the victim’s heat radiations.

As cold-blooded animals, reptiles have practically no internal metabolic mechanisms for maintaining their body temperature within physiologically safe limits. Nevertheless, reptiles, such as snakes and lizards, are able to keep their body temperature near these safe levels through behavioral regulation (i.e., by moving to cooler or warmer places as necessary). For example, through behavioral heating strategies the body temperature of the lizard Sceloporus magister was maintained at 34.9 ± 0.6 °C (94.8 ± 1.1 °F), although the average air temperature was 33 °C (91 °F). Information on behavioral thermal regulation has been recorded for the North American sidewinder, Crotalus cerastes; for example, in one study, the snake moved partially in and out of its burrow into the sun to maintain a body temperature of 31–32 °C (88–90 °F) over several hours. However, further studies discovered the ideal body temperature of C. cerastes to be about 30 °C (86 °F). The desert iguana, Dipsosaurus dorsalis, regulates its body temperature largely by behavioral mechanisms to achieve and hold body temperatures near 38.5 °C (101.3 °F). Thermal adjustments by iguanas include postural orientation to solar radiation both inside and outside burrows and altered thermal contact of the body surface with the soil.

There is some electrophysiological evidence of thermal sensitivity among amphibians; however, these organisms appear to respond only to relatively large temperature changes. The lateral-line organs in the platanna frog, Xenopus laevis, are sensitive to minute water turbulence but also respond to static temperatures and to temperature changes. However, it is not clear whether the lateral-line organ is important for thermoreception; it may function solely in rheotaxis (movement in response to currents in air or water).

In the reptilian brain the hypothalamus appears to be the most important thermoregulatory structure, acting as a central processing station for thermal information received from internal and peripheral thermoreceptors. Molecular studies have identified the presence of heat-sensing TRPV channels in some reptiles, including frogs of the genus Xenopus, the estuarine (saltwater) crocodile (Crocodylus porosus) the scincid lizard Pseudemoia entrecasteauxii, and the jacky lizard, Amphibolurus muricatus. In addition, a cool-sensing TRPM channel has been identified in C. porosus. In this crocodile, TRPV and TRPM are expressed in muscle, liver, and heart tissues. Investigations exploring the reptilian pineal gland, which controls melatonin secretion, have revealed the complexity of thermoregulation in reptiles. For example, melatonin levels are known to affect body temperature selection in reptiles. Studies into the existence of TRP channels and other cellular thermoreception mechanisms in amphibians are ongoing.