The Museum has a large and growing collection of approximately 8,000 pathological specimens, all are catalogued. The teaching collection is arranged in most part systemically but with some smaller specialised sub-collections on, for instance, Forensic Medicine and HIV - AIDS.
The Museum is arranged into four bays, each of which is divided into three floors. The two upper floors are galleries, which ring the bays and hold the specimen collections.
The Museum's collection includes the following notable specimens, artefacts, models and paintings.
The Gordon Museum has a smaller satellite collection called the Shattock Museum, which is on the St Thomas' campus. An additional satellite collection has recently been added on the Denmark Hill campus. Both of these Museums have good collections of teaching specimens.
In 2009 the Museum opened an extension – the Life Sciences Museum housing around 3,000 life sciences and zoological specimens.