:To study pain-brain morphometry associations as a function of post-surgery stages (anesthesia, pain and analgesia) in an acute pain model. :Impacted mandible third molar were extracted. Before surgery, an anatomical T1 scan was obtained. Regional brain volumen and subcortical nuclei shapes were obtained. Statistical analyses were done using multiple regression, being pain scores the predictors and voxel volumes, subcortical nuclei volumes and subcortical nuclei shapes, the outcomes. :Pain was significantly larger at pain than at anesthesia and analgesia stages, and was higher during anesthesia than during analgesia. Pain intensity was related to grey matter in several cortical (Insula, Mid Frontal and Temporal Gyruses, Precuneus, Anterior Cingulate), and subcortical nuclei (Hippocampus, Thalamus, Putamen, Amygdala), depending of the post-surgical stage. A larger number of brain areas showed significance at pain that at anesthesia and analgesia stages. :The relationships of regional brain volumes and subcortical nuclei shapes with pain scores seemed to be unsteady, as they changed with the patient's actual pain stage.