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Overcoming the Cartesian dualism of mind and body, the philosophical concept of "embodiment" not only provides a holistic theoretical framework for conceptualizing the human self as embedded in the bodily self, but also provides an integrative approach to understanding the formation of the human self, and how it changes within the matrix of social relationships. Exploring how embodiment as a guiding metaphor elucidates the multidimensional nature of depression, this article aims to offer a theoretical framework for pastoral care and counseling regarding the formation of the self and related psychopathology. Focusing on the biological dimension, this study examines how recent scientific knowledge of depression in genetic studies and molecular biology research supports the use of embodiment as a framework for conceptualizing depression, and more broadly the self and its formation. Drawing upon the psychological theories of learning and social emotions, this article will also explore how the physical body interacts with the environment by examining how the self forms, and depression develops within an embodiment metaphor. In doing so, this article presents how utilizing embodiment as a metaphor can meaningfully connect biological dimensions with psychological perspectives, such as psychodynamic and cognitive behavioral theories. This study further examines the theological and spiritual significance of embodiment in terms of theological anthropology and spiritual formation. Finally, it considers some practical implications for the holistic treatment of depression.