Vaccines currently routinely recommended to the general population in the U.S.* have not been shown to cause fibromyalgia or chronic fatigue syndrome (CFS).
The 2012 report by the Institute of Medicine (IOM), now called the National Academy of Medicine (NAM), found no relevant studies of quality in the literature assessing an association between fibromyalgia and MMR, influenza, hepatitis B or DTaP vaccines, or between CFS and MMR vaccine . One self-controlled case series published since this report found no association between CFS and bivalent HPV vaccine (Cervarix) .
The etiological causes and underlying pathogenic mechanisms of fibromyalgia and CFS are still unclear and the subject of much debate [3-5]. Theories that attempt to explain the mechanisms behind the development of these two disorders generally focus on sympathetic nervous system dysfunction, the inflammatory and oxidative stress pathways and the neuroendocrine system. Symptoms such as pain and fatigue have been associated with chronic inflammation, raised levels of oxidative stress and mitochondrial dysfunction. It has also been suggested that the hypothalamic-pituitary-adrenal axis and cortisol also have a role in the pathogenesis of fibromyalgia and CFS; however, it is still unclear whether these pathways are causes or just byproducts of these syndromes [6, 7]. Environmental stimuli such as stress or viral infection are thought to be able to trigger the pathogenesis of these disorders in genetically predisposed individuals [4, 8].
The IOM concluded that there was no mechanistic evidence for an association between fibromyalgia and MMR, influenza, hepatitis B or DTaP vaccines, or between CFS and MMR vaccine 
1. Institute of Medicine. In: Stratton K, Ford A, Rusch E, Clayton EW, eds. Adverse Effects of Vaccines: Evidence and Causality. Washington (DC): National Academies Press (US); 2012.
2. Donegan K, Beau-Lejdstrom R, King B, Seabroke S, Thomson A, Bryan P. Bivalent human papillomavirus vaccine and the risk of fatigue syndromes in girls in the UK. Vaccine 2013;31:4961-7.
3. Bazzichi L, Sernissi F, Consensi A, Giacomelli C, Sarzi-Puttini P. Fibromyalgia: a critical digest of the recent literature. Clin Exp Rheumatol 2011;29:S1-11.
4. Moss-Morris R, Deary V, Castell B. Chronic fatigue syndrome. Handbook of clinical neurology 2013;110:303-14.
5. Committee on the Diagnostic Criteria for Myalgic Encephalomyelitis/Chronic Fatigue S, Board on the Health of Select P, Institute of M. The National Academies Collection: Reports funded by National Institutes of Health. Beyond Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Redefining an Illness. Washington (DC): National Academies Press (US). Copyright 2015 by the National Academy of Sciences. All rights reserved.; 2015.
6. Romano GF, Tomassi S, Russell A, Mondelli V, Pariante CM. Fibromyalgia and chronic fatigue: the underlying biology and related theoretical issues. Adv Psychosom Med 2015;34:61-77.
7. Martinez-Martinez LA, Mora T, Vargas A, Fuentes-Iniestra M, Martinez-Lavin M. Sympathetic nervous system dysfunction in fibromyalgia, chronic fatigue syndrome, irritable bowel syndrome, and interstitial cystitis: a review of case-control studies. J Clin Rheumatol 2014;20:146-50.
8. Buskila D, Atzeni F, Sarzi-Puttini P. Etiology of fibromyalgia: the possible role of infection and vaccination. Autoimmun Rev 2008;8:41-3.