There are many possible causes of the complex of symptoms, especially chronic pain, that together we call fibromyalgia — so let's dive in.
Several rheumatic conditions cause pain and tenderness in the muscles or joints, just like fibromyalgia. A few examples include rheumatoid arthritis, lupus, scleroderma, and polymyositis, but there are many more.
What these conditions all have in common is an autoimmune reaction, in which the body's own immune system attacks some part of the connective tissue that holds things together. These attacks cause the tissues to become inflamed, and this inflammation in turn causes pain, usually associated with some degree of swelling, redness, or fever.
Most doctors don't call the pain from these autoimmune conditions "fibromyalgia," especially because the signs of fibromyalgia don't include inflammation.
But if you didn't know about the underlying rheumatologic diagnosis, and especially if there isn't any swelling or redness to indicate inflammation, it would be hard to tell the difference.
Hormonal abnormalities can also cause pain, fatigue, and weakness. Hypothyroidism (underactive thyroid) is the most common example. Other symptoms of hypothyroidism might include weight gain, fluid retention, constipation, and feeling cold — none of which are very specific and often overlap with features of fibromyalgia.
Cushing syndrome (overproduction of cortisol) and hyperparathyroidism (overactive parathyroid) can also cause similar symptoms. Vitamin D deficiency, which is technically not a hormonal abnormality, can cause hyperparathyroidism and chronic pain, too.
For decades, various infections have been associated with both fibromyalgia and chronic fatigue. Many doctors and patients have suspected chronic infection with the Epstein Barr virus (the cause of infectious mononucleosis).
More recently, there has been speculation that the bacterium that causes Lyme disease remains alive in the body and causes fibromyalgia and chronic fatigue.
Quality medical research has shown that such patients do not have ongoing infection with these organisms, although chronic pain can be triggered by these and other infections.
Some patients do report feeling better when they take antibiotics for a long time. However, that doesn't prove that infection is the culprit — the improvement could be due to a general anti-inflammatory effect of some antibiotics, or even to a placebo effect — and there are significant risks to prolonged antibiotic use.

