Joint pain causes can be divided into several categories.
Infections such as viruses (in particular, parvovirus) can cause a type of arthritis. Bacteria such as gonococcus (the bug that causes gonorrhea) and Borrelia, the organism that causes Lyme disease, are well known infectious causes for joint pain.
Trauma is an obvious cause. This can range from an athletic injury occurring more than 30 years ago leading to osteoarthritis in the knee to a whiplash injury that happened yesterday accounting for total body stiffness and pain today!
Disorders of the blood are an uncommon but important cause of joint pain. Leukemia and lymphoma can present as aches and pains. Often fever, sweats, and weight loss accompany the pains... but not always. Multiple myeloma- a malignancy that affects the plasma cells in the blood- causes ill-defined joint pains. Sickle-cell anemia and hemophilia both are associated with arthritis. A blood disorder due to excess iron in the blood- hemochromatosis- is responsible for causing both cirrhosis of the liver as well as an unusual type of arthritis.
Endocrine problems can cause aches and pains. For example, growth hormone excess is called acromegaly. This is a cause of terrible arthritis. Thyroid hormone deficiency also causes aches and pains that mimic the symptoms of fibromyalgia
Closely related to endocrine causes are the metabolic disease like gout and pseudogout which cause inflammatory types of arthritis.
The largest category of causes of aches and pains is arthritis. Wear and tear arthritis- termed osteoarthritis- is the most common form of arthritis. This arthritis is due to premature wearing away of cartilage, the gristly that protects the end of long bones. Osteoarthritis most often affects weight bearing areas such as the neck, low back, hips, and knees. It also affects the hands and feet. More autoimmune types of arthritis such as systemic lupus erythematosus, scleroderma, polymyalgia rheumatica, psoriatic arthritis, and rheumatoid arthritis can cause severe total body aches and pains in the joints. These autoimmune diseases have more inflammation associated with them. In addition, constitutional symptoms such as low grade fever, weight loss, sweats, and fatigue are common.
Finally soft tissue rheumatism - termed fibromyalgia- is a very common reason for a person to have "total body joint pain". While not a life-threatening disorder, fibromyalgia, which is often accompanied by fatigue, short term memory loss, "fibro fog", and bladder and bowel disturbance is can be debilitating.