Abstract Objective Though cigarette smoking (CS) is a well‐known risk factor for ischemic stroke (IS), there is no data on how CS affects the blood transcriptome in IS patients. Methods We recruited IS‐current smokers (IS‐SM), IS‐never smokers (IS‐NSM), control‐smokers (C‐SM), and control‐never smokers (C‐NSM). mRNA expression was assessed on HTA‐2.0 microarrays and unique as well as commonly expressed genes identified for IS‐SM versus IS‐NSM and C‐SM versus C‐NSM.