The Department of Animal Reproduction, Gynaecology, and Obstetrics, earlier known as the Department of Animal Reproduction, came into existence in the year 1958-59. Before its establishment, the Cattle Sterility Scheme of the Bombay State was functioning in the college and catering to the whole of the then Bombay State. The Government of India, on the advice of the FAO Expert Late Prof. Emeritus Nils Lagerlof, directed the States and Universities to establish a separate Department of Obstetrics and Gynaecology. Accordingly, the post of Professor of Gynaecology was created by the Government of Bombay State, and the first to occupy the chair in 1958 was Prof. C. R. Sane, a pioneer of the Artificial Insemination programme in the State in 1950, who also had specialized training in the Physio-Pathology of Reproduction in Sweden.

Under the leadership of Prof. C. R. Sane, the undergraduate training programme started in 1958 by establishing a small unit with bulls and cows to impart practical training. In 1961, the postgraduate programme (M.V.Sc.) was initiated. In the late 1960s, Ph.D. by research was started and continued until 1994. Kokan Krushi Vidyapeeth began offering a Ph.D. in Animal Reproduction by coursework in 1995-96, and the same has continued after the inception of MAFSU in 2000. So far, 123 students have obtained M.V.Sc. degrees, and 14 students have been awarded Ph.D. degrees—7 by research and 7 by coursework.

A close liaison with the State Animal Husbandry Department for field problems of infertility in livestock, established during Dr. C. R. Sane's tenure, still continues. This collaboration has helped uncover many infertility problems and develop remedial measures. Topics addressed include prolonged postpartum anoestrous condition in bovines, Vibriosis, Leptospirosis, anaerobic infections, copper deficiency, nutritional and hormonal factors in reproduction, estrus induction and synchronization, repeat breeding issues, parturition processes in different species, male sexual behavior, semen transport and preservation, male infertility, and advances in disease diagnosis and treatment using ultrasound and vaginoscopy. Companion animal fertility and infertility management and artificial insemination in canines are also highlights of the department's work.

The undergraduate courses are conducted in the 7th, 8th, and 9th semesters. In addition to regular laboratory work, students receive hands-on training at the Instructional Livestock Farm Complex and have a unique opportunity to examine genital organs at the Deonar Abattoir. Undergraduate students are also exposed to clinical cases at the TVCC.

Departmental staff members and postgraduate students regularly visit cattle breeding farms and stables in and around Mumbai, including a farm at Igatpuri, to participate in sexual health control programmes such as pregnancy diagnosis, infertility treatment, insemination, and pre- and postpartum treatments. They also attend gyneco-clinical cases at SPCA Hospital and the department's referral clinic, providing materials for postgraduate research and boosting students' confidence to work independently.

The department has maintained a close association with Mumbai Gowrakshak Mandali since 1972, which operates cattle breeding farms at Kandivali and Betegaon housing 800 cattle. This organization provides scholarships to undergraduate and postgraduate students of MAFSU. To date, 25 M.V.Sc. and 5 Ph.D. students across various disciplines have conducted their research work at these farms.

The Indian Council of Agricultural Research (ICAR), New Delhi, sanctioned the implementation of the "Network Programme of Embryo Transfer Technology in Animal Production" during the VIII Five Year Plan (1992-97) at this department. This programme continued until 2002. Additionally, three ad-hoc schemes amounting to ₹40 lakh were sanctioned by ICAR in 1998, enabling the department to establish ultrasonography, laparoscopy, and IVM/IVF laboratories. The availability of these modern facilities strengthened the department's research output.

The department's vast teaching and research experience culminated in the publication of a comprehensive textbook, "Reproduction in Farm Animals (Theriogenology)," in 1982. This book, the first of its kind under Indian conditions, contained 891 pages, 285 illustrations, 38 tables, and nearly 300 references. The second edition, published in 1994, included four new chapters and incorporated the latest research findings.

The department played a leading role in establishing the Indian Society for the Study of Animal Reproduction (ISSAR). The Indian Journal of Animal Reproduction, the official organ of ISSAR, was launched with a key role played by this department. The responsibility for running the journal and society was shouldered by the department for over a decade since its inception.

This department has organized significant events such as the All India Symposium on Animal Reproduction in December 1981, the 1st Asian Congress on Animal Reproduction in December 1985, and the Annual Convention of the Indian Society for Buffalo Development in 2006.

The department's staff actively participate in shibirs, farmers' rallies, infertility camps, and seminars organized by Zilla Parishads and the Director of Animal Husbandry, Pune. The department investigates infertility problems referred by government, semi-government, and non-government organizations. It also regularly trains Livestock Development Officers (LDOs) on ultrasonography and artificial insemination. Over 150 LDOs have been trained in ultrasonography, and more than 500 LDOs and Livestock Supervisors (LSS) have attended artificial insemination training sessions.

The department provides consultation services to dairy farms and companion animal owners for fertility management. These services include ultrasonography in cows, buffaloes, sheep, goats, bitches, cats, and occasionally wild animals; vaginal cytology in companion animals; semen evaluation in dogs and farm animals; artificial insemination in bitches and large animals; pregnancy diagnosis; and the examination and treatment of infertility and reproductive disorders using vaginoscopy in large and small animals.