Department of Anatomy (previously called the Department of Anatomy, Embryology and Anthropology) was established in 1946 in Klaten and chaired by Prof Drs R. Radiopoetro. In 1949, the Department of Anatomy was moved to Mangkubumen and in 1980, the department moved once again to a new integrated campus in Sekip.

This department has a long journey in “Tri Dharma” which consists of education, research and public service. In education, Anatomy as a main basic science in medicine plays an important role in the development of curriculum and learning method. In the old days, students had the opportunity to do cadaver dissection in cadaver. Nowadays, prosection method is applied in teaching anatomy. Problem Based Learning (PBL) and Competence Based Curriculum (CBC) give influence in driving innovation in Anatomy. Almost all academic staff always contribute to curriculum development and become Block Coordinator Team in this PBL era.Basic anatomy is given for the first year student,continued with clinically oriented anatomy approach for the second and third year medical student.This department also produces many learning resources such as books, atlas, mannequin and replicas. Beyond Universitas Gadjah Mada, the Department of Anatomy also pioneers innovation in learning-teaching system in other Faculties of medicine in Indonesia, such as as in the University of Hasanuddin, University of Sriwijaya, University of Diponegoro, Universitas Negeri Surakarta, University of Syah Kuala, and University of Lambung Mangkurat, Universitas Muhammadiyah Yogyakarta, Indonesian Islamic University and University of Tadulako. This department also contributes to postgraduate and and clinical specialist education, such as in neurology, oral surgery, forensic, obstetrics and gynecology, earnose-throat, and surgery.

Department of Anatomy has been internationally recognized as a research center in Anthropology, especially with the presence of Biopaleoanthropology laboratory led by Prof. dr. T. Jacob. Other faculty members, such as Prof. Soemijati Ahmad, dr Rismanto, dr Suryadi, dr Mansyur Romi conducted embryology and genetic research. Prof Soedjono Aswin established neuroanatomy and neuroscience research which is now continued by Dr Dwi Cahyani Ratna Sari. Prof Soebijanto, Dr. A. Pratiknya and Dr Djoko Prakosa established macroanatomy science, continued by dr. Dwi Yatmo and dr Santosa Budiharjo. Dr Djoko Prakosa was pioneering the development of Bengkel Anatomy to provide medical learning resources in the application of anatomy science. Recently, Molecular medicine, translationalresearch and clinically applied anatomy are being conducted at Department of Anatomy, initiated by the younger staff such as, dr Arfian, dr Junaedy, dr.Dian Prasetyo and dr Yana. Translational research and molecular medicine also become essential development in anatomy research. Development of disease model based on anatomical science combined with molecular approach poses a great challenge to improve research in Anatomy department, Faculty of Medicine.

Community service activities are carried out through implementation in fitness and renal health awareness programs, anatomy museum exhibition, health counseling and promotion, and collaboration with other professional and non-government organizations.