Core temperature is the temperature of an organism at which it is meant to operate. It tends to refer to the temperature of organs and parts of the body that are well insulated, as opposed to the skin and other surface areas, which fluctuate much more wildly. It differs from species to species, but is always the temperature at which everything works best.
Mammals regulate their core temperature with a system of thermoregulatory processes, intended to keep everything in homeostasis. When the body heats up because of external pressures, internal mechanisms cool everything down to ensure the body functions at its best. Similarly, when the external environment becomes colder than the organism, internal processes heat everything up.
This temperature is measured in a number of different ways. The easiest traditional method of measurement was with a thermometer placed under the tongue and kept there for a bit. Oral temperature is notoriously unreliable; however, and is subject to any number of interferences. Rectal temperature is considered much more reliable, albeit somewhat more difficult to obtain. There are also modern thermometers which are meant to be used in the ear, which use infrared lasers to determine the temperature of the tympanic membrane. Although ear thermometers are very convenient, many studies have found them to be quite fickle, and they are not recommended as a method of determining fever.
The average normal human core temperature is around 98.2 F (36.8 C), plus or minus 1.3 degrees Fahrenheit (0.7 C) when taken orally, and about 1.0 F (0.5 C) higher when taken rectally. Humans' temperatures actually fluctuate over the course of a day, becoming higher when a person is more active, and dropping to its lowest point halfway through the sleep cycle. Traditionally, the average human temperature was given as 98.6 F, which is a conversion of an earlier measurement from the 19th century.
Core temperature is monitored by nerve cells throughout the body. When they detect a change in temperature from the ideal, the nerve cells in the hypothalamus of the brain respond by either speeding up or slowing down in their impulse generation.
This means that when the body starts to get cold, and the core temperature starts to go lower than its ideal, the nerve cells speed up, and the body begins to shiver. Shivering in turn generates heat, which heats the body. Blood vessels are also contracted, so that less blood comes to the skin from the core, and there is less loss of heat. When the body detects that it is getting colder, it also makes hairs on the skin stand up on end. In mammals with a lot of hair, this traps air, which acts as a layer of insulation. In humans, because we have little hair left, it expresses itself only as goose bumps, and doesn’t help much in heating up the inner body.
Fever is brought on when the body essentially changes what it thinks the core temperature should be. Suddenly it wants the body to be hotter than it normally would be, usually to try to drive out some sort of hostile invader. The normal reactions still apply: shivering, reduced blood flow, etc., but now it drives the temperature up well beyond what it is meant to operate at.