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Aims/Background Previous research has shown that smoking tobacco is associated with changes or differences in brain volume and cortical thickness, resulting in a smaller brain volume and decreased cortical thickness in smokers compared with non-smokers. However, the effects of smokeless tobacco on brain volume and cortical thickness remain unclear. This study aimed to investigate whether the use of shammah, a nicotine-containing smokeless tobacco popular in Middle Eastern countries, is associated with differences in brain volume and thickness compared with non-users and to assess the influence of shammah quantity and type on these effects. Methods Male shammah users (aged 20 to 47 years, n = 30) and non-users (n = 39) underwent 1.5T magnetic resonance imaging (MRI) scans, and cortical brain volumes and thicknesses were measured using FreeSurfer. Results Significant differences were found in the volume of the right pallidum ( p = 0.02), total pallidum ( p = 0.02), total ventricle ( p = 0.02), middle posterior corpus callosum ( p = 0.04), and brainstem ( p = 0.02) between shammah users and non-users. Furthermore, yellow shammah users exhibited smaller volumes in the right lateral ventricle ( p = 0.02), total lateral ventricle ( p = 0.03), and right putamen ( p = 0.02) compared with users of other types of shammah. Regarding cortical thickness, significant differences were observed in the right medial orbito-frontal thickness ( p = 0.03), left rostral middle frontal thickness ( p = 0.03), and right rostral anterior cingulate thickness ( p = 0.04). Conclusion These findings shed light on the potential neurobiological effects of shammah use, particularly the yellow shammah, and highlighting the need for further research to fully understand its implications for brain structure and function.