Rhythms observed in nature continue in the laboratory even under constant experimental conditions such as constant light (LL) or constant dark (DD). The persistence of these rhythms is seen as proof of endogenous biological clocks. When in constant conditions away from any external cues, these rhythms are called freeruns.

Changes in period length

A natural freerun rhythm rarely follows an exact 24 hour cycle, but instead has a period within the vicinity. Freerunning rhythms have evolved to be close to 24 hours but not exactly so that there is a stable phase relationship between the circadian oscillator and the required external cycle.

Biological clocks are not that accurate compared to mechanical clocks. A freerunning circadian rhythm may change the length of its period over a course of months or years. For example mice freerunning in DD had period lengths that continued to shorten even after 300 days. The reason for these changes are unclear, and are called spontaneous changes (Binkley 1997).

Pretreatments and aftereffects

It is possible to alter the lengths of the freerunning period cycle by using pretreatments. These are changes in the environmental conditions such as a light pulse or a transfer from a light-dark cycle to constant dark. The resulting alterations in the period length are called aftereffects. These after effects are not always constant. For example sparrows placed in constant dark after a cycle of LD 12:12 start to freerun with a period shorter than 24 hours. Over time the length of the period increases, a phenomenon known as a knee (Binkley 1997)

The length of a photoperiod can also affect the period length of a freerunning cycle. In sparrows the aftereffect period length was less when the sparrow was first exposed to a cycle of LD 16:8 than when the cycle was LD 8:16. In fact other changes in the overall period can have an effect on the aftereffects e.g. non 24 hour cycles. Period lengths in hamsters kept in constant dark are longer after they are entrained to 25 hour LD cycles than if they are exposed to 23 hour LD cycles (Binkley 1997).

Activity time and rest time

In a freerunning cycle, the period length (T) is divided into two areas: activity time (designated alpha), when the organism is active and rest time (designated rho) when it is not. In humans alpha is the time when we are awake, and rho is the time when we are asleep.  The duration of these to parts is subject to environmental conditions and whether the animal in question is diurnal or nocturnal.

In nocturnal animals on a normal light-dark cycle, the animal is active in the dark and rests when it is light. In constant dark when its cycle is freerunning, its activity time is larger. With diurnal animals activity time is increased in constant light. Activity time can also be altered by the intensity of light, with an increased activity time in bright light than in dim light.

Period length my also be affected in different ways by different conditions in nocturnal and diurnal creatures. Diurnal animals have an increased period length when they freerun in constant dark and a decreased period length in constant light. This is reversed in nocturnal animals where the freerunning period length increases in constant light and decreases in constant dark.