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The concept of Self-Compassion has recently gained significant importance in research and psychotherapy. However, little is known about its neural correlates. Related constructs, such as compassion for others, empathy, and emotion regulation, have been repeatedly associated with structural correlates in subcortical brain regions - including the amygdala, hippocampus, and insula - but corresponding associations with Self-Compassion have not been examined yet. Therefore, this study investigated the potential association between Self-Compassion and brain structure. Structural MRI data from N = 301 (gender (m/f): 106/195) healthy participants were analyzed. Threshold-free cluster enhancement (TFCE) corrected voxel-wise multiple regression analyses of the Self-Compassion Scale and its two subscales (Self-Compassionate Attitude and Self-Critical Attitude) on gray matter volume (GMV) were conducted separately within the bilateral amygdala, hippocampus, and insula as regions of interest (ROIs). An exploratory whole-brain analysis was performed for all three models. Significance threshold for all analyses was p_FWE < .05. The analysis revealed a significant negative association between Self-Compassion and the GMV in the left amygdala (k₌ 94, t₂₉₆ = 2.53, p_TFCE-FWE =.042). Further, a significant negative association was found between Self-Compassionate Attitude and GMV in the bilateral amygdala (k = 196, t₂₉₆ = 2.59, p_TFCE-FWE =.032; k = 63, t₂₉₆ = 2.53, p_TFCE-FWE =.043). No other significant associations were observed (all p ≥ .080). The findings indicate initial evidence that Self-Compassion, as well as Self-Compassionate Attitude, is associated with subcortical brain structures involved in emotion processing, indicating a relevance of Self-Compassion with regard to emotional encoding and appraisal.