Some of these disease criteria overlap, further complicating the diagnostic workup in patients with a potential CTD. Unclassifiable symptoms, physical examination findings, or serological results suggestive of a CTD frequently lead to diagnoses such as incomplete lupus, latent lupus, overlap syndrome, and undifferentiated connective-tissue disease (UCTD). Conceptually, these terms may seem synonymous; however, specific definitions are necessary for appropriate diagnostic, therapeutic, and prognostic determinations.

Scleroderma is an autoimmune disease of the connective tissue featuring skin thickening, spontaneous scarring, blood vessel disease, varying degrees of inflammation, associated with an overactive immune system. Autoimmune diseases are illnesses which occur when the body's tissues are attacked by its own immune system. Scleroderma is characterized by the formation of scar tissue (fibrosis) in the skin and organs of the body. This leads to thickness and firmness of involved areas. Scleroderma, when it's diffuse or widespread over the body, is also referred to as systemic sclerosis.

The cause of scleroderma is not known. Researchers have found some evidence that certain genes are important factors, but the environment seems to also play a role. The result is activation of the immune system in a susceptible individual, causing injury to tissues that result in injury similar to scar-tissue formation. The fact that genes seem to cause a predisposition to developing scleroderma means that inheritance at least plays a partial role. It is not unusual to find other autoimmune diseases in families of scleroderma patients. Some evidence for the role genes may play in leading to the development of scleroderma comes from the study of Choctaw Native Americans who are the group with the highest reported prevalence of the disease. The disease is more frequent in females than in males.

Lupus is an autoimmune disease characterized by acute and chronic inflammation of various tissues of the body. Autoimmune diseases are illnesses that occur when the body's tissues are attacked by its own immune system. The immune system is a complex system within the body that is designed to fight infectious agents, such as bacteria and other foreign microbes. One of the ways that the immune system fights infections is by producing antibodies that bind to the microbes. People with lupus produce abnormal antibodies in their blood that target tissues within their own body rather than foreign infectious agents. Because the antibodies and accompanying cells of inflammation can affect tissues anywhere in the body, lupus has the potential to affect a variety of areas. Sometimes lupus can cause disease of the skin, heart, lungs, kidneys, joints, and/or nervous system. When only the skin is involved, the condition is called lupus dermatitis or cutaneous lupus erythematosus. A form of lupus dermatitis that can be isolated to the skin, without internal disease, is called discoid lupus. When internal organs are involved, the condition is referred to as systemic lupus erythematosus (SLE).