Abstract Background Previous research has shown an association between thalamus and cognition in Parkinson’s disease (PD). Objectives To investigate the microstructural integrity of the nuclei of the thalamus and relationship with cognition. Methods Level II Movement Disorder Society Task Force Criteria characterised patients with Parkinson’s disease as cognitively normal (PDN, n=51); with mild cognitive impairment (PD-MCI, n=16) or with dementia (PDD, n=15). Twenty-three healthy control subjects were included for comparison. A k -means clustering approach segmented the thalamus into regions representing nine major nuclei. Volume, fractional anisotropy and mean diffusivity of nuclei were compared between cognitive groups and the relationship with cognitive domain z-scores investigated using hierarchical Bayesian regression models. Results There was an overall progressive increase in mean diffusivity as cognition deteriorated (PDN: 1.4 µm 2 /s (95% uncertainty interval [0.2, 2.7]), PDMCI: 2.4 µm 2 /s [0.8,4.0], PDD: 4.5 µm 2 /s [2.8, 6.3]). The largest increase was in the lateral dorsal nucleus (PDN: 0.3 µm 2 /s [-6.7, 7.2], PDMCI: 5.4 µm 2 /s [-4.7, 16.1], PDD: 14.8 µm 2 /s [5.0, 25.0]). Fractional anisotropy showed minimal change between cognitive groups (PDN: 0.001 [-0.005, 0,007], PDMCI: −0.005 [-0.013, 0.003], PDD: −0.005 [-0.014, 0.003]). Increase in mean diffusivity of the thalamus is associated with a global decline in cognition, the magnitude of the effect was greatest in lateral dorsal nucleus. Fractional anisotropy only showed evidence of a relationship with cognitive domain scores in the lateral dorsal nucleus. Conclusions The relationship between lateral dorsal nucleus integrity and cognitive changes is likely due to its primary connectivity with frontal and temporal regions.