Since the beginning of his activities at Imam Khomeini Hospital in 2000, Dr. Ghaffari had always had a plan to establish a comprehensive genetic center at the university. In this regard he pursued this idea and designed and launched the Molecular Genetic Lab at the Cancer Institute, , the Shariati Hospital Genetic counseling Clinic, Reproductive Health Research Center Genetic counseling Clinic, and developed Genetic counseling Clinic of Imam Hospital and Cytogenetic Lab of the Cancer Institute. Finally, with the consolidation of all the above activities, and a new fund received from the Ministry of Health, an integrated facility was established in 2006. The center was eventually formally launched in 2008 with the presence of the chancellor of the Tehran University of Medical Sciences.
As a first academic comprehensive Iranian genetic center, at the time, it was known as the center of excellence for its extensive activities and modern equipment, as well as its establishment in a state hospital (the Imam Khomeini Hospital complex). The center worked closely with the specialized departments of nearly all medical fields . The center was mainly consisted of two departments namely: Genetic Counseling department and the Clinical Genetics Laboratory.
Services provided at this center include: Genetic counseling and clinical genetic services such as pre-marital genetic counseling, preconception and prenatal genetic counseling, laboratory genetic services include: molecular genetics, cytogenetics (chromosomal aberrations), molecular cytogenetics, and FISH laboratory (for the diagnosis of cancers, fetal health, and … before implantation). Under Dr Ghaffari, the center regularly provided clinical genetic courses for prenatal and neonatal fellowship clinicians and genetic counseling courses for MSc and PhD students of medical genetics of Tehran and Tarbiat Modarres universities. The center established research collaboration with Tehran university of Medical Science and ministry of health for a wide range of research projects in the field of mental retardation, hereditary hearing impairment, inherited eye disorders, musculoskeletal disorders and etc. Dr. Ghaffari was in charge of this center until the spring of 2010, and after ten years in Imam Khomeini Hospital following the successful holding of the 2nd Medical Genetic Congress, he returned to the Department of Genetics at Tehran University of Medical Sciences.