Alopecia Areata is widely believed to be an autoimmune disease. A breakdown in the immune system results in autoimmunity. Essentially every individual produces various cell types that fight disease and infection. There are all sorts of immune cells such as lymphocytes, monocytes, macrophages and other cells, all of which have different roles to play in fighting off infection. To fight invading organisms the immune cells must be able to recognize bacteria (or whatever) as foreign and not part of the individual’s own body. They do this by recognizing structures called antigens (antigens are usually proteins) on the surface of the invader. Every individual organism, including our ourselves, has a different set of antigens and the immune system as a whole can recognize all antigens with different immune cell clones/types recognizing different antigens. So Alopecia Areata in this case is regarded as an autoimmune disease where hair follicles in the Anagen stage are being mistakenly attacked by the cells of the immune system. The main idea of this clinical condition is that affected by Alopecia Areata hair follicle cells after attacks of the immune system of forced to leave Anagen stage, enter into Catagen and then immediately move into the Telogen / Exogen stages. This causes hair loss at the certain scalp location where usually appears the very first spot. In the future such a spot may be distributed in the form of wave. Hair follicles can once again return to the next Anagen stage, but after the immune system cells attack hair follicles produce already weak and modified hair. These hair follicles are characterized as a dystrophic Anagen phase follicles. Damaged hair follicles may continue to vary between the different duration cycles of formation - between Anagen and Telogen stages. In fact it has not yet been determined what effects definetely enable and provoke an appearance of Alopecia Areata. There are several suggested factors that may influence the course of disease:

 

Psychologic long term chronic stress is an important precipitating factor in Alopecia Areata. Stress is suggested as an environmental trigger in people predisposed to Alopecia Areata development (due to genetic susceptibility for example) rather than the primary basis for disease to develop. 
Shock and sudden extreme stress: there have been a number of reports on individual cases where clearly defined sudden stress events have preceded Alopecia Areata development. The emotional trauma of a family death or being involved in a car accident without major injury have been suggested as triggers for a disease onset. 
Physical trauma can trigger the onset of disease as anything that stimulates the immune system from being hit on the head to an infection can be a potential trigger.

Local skin injury - cuts, scrapes, and other abrasions of normal haired skin are often the focus for the onset of a new patch of hair loss in Alopecia Areata susceptible people. Ironically, similar abrasions in areas of skin already affected by Alopecia Areata can be the focus of temporary hair regrowth. Injury is known to promote Anagen hair follicle growth in skin immediately surrounding the injured site.

Genetic predisposition - it has been shown that there is a higher incidence of Alopecia Areata occurring in genetically related individuals. This suggests that at least some people are genetically predisposed towards the development of Alopecia Areata. It has been found that some genes to be much more common in people with Alopecia Areata so it is generally believed that Alopecia Areata susceptibility is polygenic - there are a number of genes which, if present, make that individual more likely to develop Alopecia Areata. The triggers for the actual onset of Alopecia Areata are most likely environmental but susceptibility to development of Alopecia Areata, its resistance to treatment, persistence, regression and extent over the body might be influenced by the presence and interaction of several genes.

Viral/bacterial infection - general viral/bacterial infections may promote the immune system into an inappropriate response against hair follicles in susceptible people. 
Pregnancy/hormones - an apparent link between hormonal fluctuations and Alopecia Areata onset has been recognized especially during late stages of pregnancy. Women who already have Alopecia Areata can find that they have complete, but temporary, hair regrowth around the time of childbirth. Puberty and menopause have also been suggested as a time of potential disease onset or remission.

Allergies - statistical analysis shows that Caucasians with Alopecia Areata and some form of atopy (asthma, eczema, rhinitis) are inclined to have hair loss that is more extensive and/or of prolonged duration. Interestingly, statistical analysis of Indians with alopecia areata showed no such link. This may suggest that the different genetic composition of different races must be taken into account when explaining susceptibility to Alopecia Areata development.

Chemicals - one "outbreak" of Alopecia Areata in workers at a water treatment plant in a paper factory was linked to long term exposure to the chemical acrylamide. Formaldehyde and pesticides have also been suggested as a potential influence in the development of Alopecia Areata. There are reports suggesting a link between Alopecia Areata development and zidovudine treatment of HIV and Fluvoxamine anti-depressive treatment.

Seasonal changes - a significant number of people with Alopecia Areata find the extent of the hair loss cycles in time with the seasons. Some people find the hair loss is much more extensive in winter and have temporary, partial regrowth in summer.