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Despite compelling evidence that cigarette smoking impacts the risk of developing multiple sclerosis (MS), little is known about smoking-associated changes in the primary exposed lung cells of patients. We aimed to examine molecular changes occurring in bronchoalveolar lavage (BAL) cells from MS patients in relation to smoking and in comparison to healthy controls (HCs). We profiled DNA methylation in BAL cells from female MS ( = 17) and HC ( = 22) individuals, using Illumina Infinium EPIC and performed RNA-sequencing in non-smokers.