The palaeontological collection contains over 1 million fossils, collected from all over the world, tracing the history of life on Earth from over 3000 million years ago to the present day.

When Adam Sedgwick became Woodwardian Professor in 1818 the Museum held around 10,000 fossils. Sedgwick was responsible for greatly expanding the fossil collection through donations and purchases. He was well acquainted with a number of collectors of the period, including Mary Anning, from whom he purchased several ichthyosaur specimens, now on display in the Museum. By the time of his death in 1873 the collection had grown to nearly half a million specimens.

The collections contains over 7,000 British type specimens (specimens used to describe a new species) and over 21,000 specimens illustrated in the scientific literature. The collection is still growing, mainly as a result of the research activities of the Department of Earth Sciences. Material is also acquired from other scientific institutions and members of the public.

The Museum holds a large collection of fossils reflecting the geology of Cambridgeshire and its region. Many of these are related to the local exploitation of mineral resources in the area for example brick making (Oxford and Kimmeridge Clay fossils) and phosphate mineral extraction and cement manufacture (Neolithic - Bronze Age peat, River Cam gravels and Cambridge Greensand fossils).