Autoimmune diseases arise from an overactive immune response of the body against substances and tissues normally present in the body.  Today there are more than 40 human diseases classified as either definite or probable autoimmune diseases and they affect 5-7% of the population.  Almost all autoimmune diseases appear without warning or apparent cause and most patients suffer from fatigue.
Source: Wikipedia Autoimmune Disease 

A process in which the body’s immune system causes illness by mistakenly attacking healthy cells, organs, or tissues in the body that are essential for good health.  Multiple sclerosis is believed to be an autoimmune disease, along with systemic lupus erythematosus, rheumatoid arthritis, scleroderma, and many others. The precise origin and pathophysiologic processes of these diseases are unknown.
Source:  The National MS Society

The word "auto" is the Greek word for self. The immune system is a complicated network of cells and cell components (called molecules) that normally work to defend the body and eliminate infections caused by bacteria, viruses, and other invading microbes.  If a person has an autoimmune disease, the immune system mistakenly attacks self, targeting the cells, tissues, and organs of a person's own body.  A collection of immune system cells and molecules at a target site is broadly referred to as inflammation.

Source:  Understanding the Immune System NIAID

Source:  Understanding Autoimmune Disease NIAID

Source:  Lab Tests Online