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Diminished motor cortical excitability, as a measurement of increased resting motor threshold (RMT) with transcranial magnetic stimulation (TMS), is known to be associated with chronic pain conditions. This study compared RMT in Veterans with GWI related diffuse body pain including headache, muscle and joint pain with their military counterparts without GWI related diffuse body pain. Single pulse TMS was administered over the left motor cortex, using anatomical scans of each subject to guide the TMS coil, starting at 25% of maximum stimulator output (MSO) and increasing in steps of 2% until a motor response with a 50\u00a0\u00b5V peak to peak amplitude, defined as the RMT, was evoked at the contralateral flexor pollicis brevis muscle. RMT was then analyzed using Repeated Measures Analysis of Variance (RM-ANOVA). Veterans with GWI related chronic headaches and body pain (N\u2009=\u200920, all males) had a significantly (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.001) higher average RMT (%\u2009\u00b1\u2009SD) of 77.2%\u2009\u00b1\u200916.7% compared to age and gender matched military controls (N\u2009=\u200920, all males), whose average was 55.6%\u2009\u00b1\u20098.8%. Veterans with GWI related diffuse body pain demonstrated a state of diminished corticomotor excitability, suggesting a maladaptive supraspinal pain modulatory state. The impact\u00a0of this observed supraspinal functional impairment on other GWI related symptoms and the potential use of TMS in rectifying this abnormality and providing relief for pain and co-morbid symptoms requires further investigation.<\/jats:p><jats:p><jats:bold>Trial registration<\/jats:bold>: This study was registered on January 25, 2017, on ClinicalTrials.gov with the identifier: NCT03030794. Retrospectively registered. <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/clinicaltrials.gov\/ct2\/show\/NCT03030794\">https:\/\/clinicaltrials.gov\/ct2\/show\/NCT03030794<\/jats:ext-link>.<\/jats:p>","DOI":"10.1038\/s41598-020-75006-8","type":"journal-article","created":{"date-parts":[[2020,10,28]],"date-time":"2020-10-28T11:24:39Z","timestamp":1603884279000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Diminished corticomotor excitability in Gulf War Illness related chronic pain symptoms; evidence from TMS study"],"prefix":"10.1038","volume":"10","author":[{"given":"Karen","family":"Lei","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alphonsa","family":"Kunnel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Metzger-Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahrokh","family":"Golshan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Javors","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennie","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Vaninetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Rutledge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Leung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,10,28]]},"reference":[{"key":"75006_CR1","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1016\/j.cortex.2015.08.022","volume":"74","author":"RF White","year":"2016","unstructured":"White, R. 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