Preterm neonates are at higher risk of neurocognitive and neurosensory abnormalities. While numerous studies have looked at the effect of prematurity on brain anatomy, none to date have attempted to understand the relative pose of subcortical structures and to assess its potential as a biomarker of abnormal growth. Here, we perform the first relative pose analysis on a point distribution model (PDM) of the thalamus between 17 preterm and 19 term-born healthy neonates. Initially, linear registration and constrained harmonic registration were computed to remove the irrelevant global pose information and obtain correspondence in vertices. All the parameters for the relative pose were then obtained through similarity transformation. Subsequently, all the pose parameters (scale, rotation and translation) were projected into a log-Euclidean space, where univariate and multivariate statistics were performed. Our method detected relative pose differences in the preterm birth for the left thalamus. Our results suggest that relative pose in subcortical structures is a useful indicator of brain injury, particularly along the anterior surface and the posterior surface. Our study supports the concept that there are regional thalamic asymmetries in the preterm that may be related to subtle white matter injury, have prognostic significance, or be related to preterm birth itself.