The HEC was created in the late 19th and early 20th centuries by anatomist Charles Sedgwick Minot for the benefit of the embryological research community. Minot used archival materials and organizational principles, resulting in a well-preserved and organized collection even today. It remains of significant importance to taxonomists, historians of science, and other researchers from a variety of disciplines. 

In the early years of its existence (the first two decades of the 20th century), it was an influential locus of research. As of Minot’s death in 1914, the collection was cited in the works of at least 22 different authors. With Minot’s passing, and the decline of interest in embryological research as a whole, the collection fell into a period of disuse. It was maintained in obscurity at the Harvard Medical School for most of the 20th century. In 1992, the non-human slides were transferred from the Medical School to the MCZ, while the human embryo slides were transferred to the National Museum of Health and Medicine in Washington, D.C.

Renewed curation efforts began in earnest at the MCZ in 2010, in conjunction with a survey of collection contents and condition. Since 2010, the collection has been inventoried and databased, and its card catalog and accompanying line drawings have been scanned and associated with their relevant collection records. Currently, a conservation project is underway involving the individual cleaning of the slides and the subsequent transfer from their older (mostly original) storage cabinets to new, archival-quality cabinets. In addition, the MCZ has initiated a scanning project with the slides utilizing a high-resolution Huron Digital Pathology slide scanner, with the ultimate aim of making the collection digitally available to researchers worldwide.