A major challenge associated with understanding mild traumatic brain injury (mTBI) is the absence of biomarkers in standard clinical imaging modalities. Furthermore, the inhomogeneity of mTBI location and intensity, combined with latent symptoms further complicates identification and treatment. A growing body of evidence suggests that the thalamus may be injured or susceptible to change as the result of mTBI. A significant number of connections to and from cortical, subcortical, cerebellar and brain stem regions converge at the thalamus. Furthermore, the thalamus is also involved with information processing, integration and the regulation of specific behaviors. We use graph theory analysis to evaluate intrinsic functional networks of the left and right thalamus in mTBI subjects (N=15) and neurologically intact healthy controls (N=12). We also explore neural correlates of the thalamic network architecture with clinical assessments. Our results suggest the presence of distinct unilateral thalamic differences in mTBI subjects. We also observe correlations of the thalamic changes with clinical assessments. The findings from this study have implications for functional networks in the thalamus and its projections for application as a potential biomarker for mTBI detection.