Mitragyna speciosa (Korth.) or kratom is a native medicinal plant of Southeast Asia. Commonly used by hard labours in harsh working environment, the ingestion of brewed kratom decoction is reported to produce dose-dependent stimulant and opioid-like effects. Kratom is also regularly consumed as a pain killer and as traditional cure for common maladies such as fever and cough. However, it remains unknown whether regular consumption of kratom decoction is associated with brain abnormalities in regular users in traditional settings. Methods: A total of 14 subjects (7 regular kratom users and 7 non-kratom users) voluntarily participated in this cross-sectional study. Face-to-face interviews were conducted with kratom users to determine history of kratom use and later these respondents underwent brain magnetic resonance imaging (MRI). Results: There were no significant differences (p>0.05) in the intracranial volume (ICV), cortical volumes (frontal, parietal, temporal, occipital, or cingulate lobe), or subcortical volumes (striatum, hippocampus, or amygdala), as well as in the diffusion tensor imaging (DTI) metrics, fractional anisotropy (FA) and mean diffusivity (MD) between kratom users and the controls. Conclusion: This preliminary study showed long-term consumption of kratom decoction is not significantly associated with altered brain structures in regular kratom users in traditional settings. However, further study is needed to establish more data for kratom use and its effects.