The Department of Anatomy is a basic and pivotal department at the College of Medicine at Al-Qunfudah. It teaches the anatomical structure of the human body and the body's internal organs and describes the bones of the human structure and how to identify them. In addition, the Department of Anatomy includes the study of the applied anatomy to make use of it in the clinical phase of all clinical sciences and the study of histology which includes microscopic structure of cells and tissues of the body. Finally, the Department of Anatomy teaches embryology, which handles the description of the evolution of the body' various organs and systems during fetal intrauterine growth.

The Department of Anatomy aims to make the student acquires knowledge and skills, using the bones, the natural anatomical, the wax samples and the plastic samples along with the anatomy modern three-dimensional tables.