The minimally conscious state (MCS) has been sub-categorized in MCS plus and MCS minus, i.e. respectively with and without command following capacity. Here we aimed at characterizing differences in MCS plus as compared to MCS minus by means of functional connectivity (FC). Resting state functional magnetic resonance imagery (fMRI) was acquired in 292 MCS patients and a seed-based analysis was conducted on a convenience sample of 19 MCS patients (10 MCS plus and 9 MCS minus) and 35 healthy controls. We investigated the left and right frontoparietal networks (FPN), the auditory network and the default mode network (DMN). We employed a ROI-to-ROI analysis and a voxel-based morphometry in order to investigate the inter-hemispheric connectivity and the grey and white matter volume, respectively. A significantly higher FC was found in MCS plus as compared to MCS minus in the left FPN, specifically between the left dorso-lateral prefrontal cortex and the left temporo-occipital fusiform cortex (TOFC). The FC of auditory network, right FPN and DMN, inter-hemispheric connectivity and structure of grey and white matter did not show differences between patients groups. The clinical sub-categorization of MCS is therefore sustained by FC differences in a language-related executive control network. These patient groups are not differentiated by networks involved in auditory processing, perception of surroundings and internal thoughts, nor by differences in inter-hemispheric connectivity and in morphology