With the exception of the micromounts (described right) the collection is catalogued as a single entity but is physically organized into several sub collections. Notable holdings include the minerals from the zinc mines at Franklin, New Jersey (~4,000 specimens), from the Tsumeb mine in Namibia (900 specimens), and from the local New England region (~7,000 specimens). Gemstones (~2,500 specimens) were formerly included in the mineral collection but have been organized as a separate collection.

The Systematic series is organized chemically. About 4,000 of the finest specimens are displayed in the HMNH mineral gallery. The rest - the "working" collection - is housed in readily accessible drawers.

It archives specimens used in past studies, holds material for future use, and seeks species not currently represented and other specimens suitable for investigation or exhibit. This is the primary and largest part of the mineral collection.

The Paragenetic series are suites from particular occurrences assembled to study how minerals form. These are fundamentally geological in nature as opposed to the chemical character of the systematic series. For thirty years or more Professor Palache assigned paragenetic suites that he'd field collected in New England to his Advanced Mineralogy class for term papers, several of which were later published. Building on this foundation most of the specimens from the New England region have been physically moved into the paragenetic suites both to place them in their geological context and to gain precious space in the cabinets holding the systematic series.

Micromount collections consist of small mineral specimens mounted in one-inch boxes for viewing through a microscope. The historic micromount collection (~3200 mounts) is part of A.F. Holden's personal collection left to the University in 1912. The Reverend G.G. Rakestraw's collection with its accompanying Zentmeyer binocular microscope and library was transferred to the Collection of Historical Scientific Instruments in August 2004. During the 1990s a contemporary micromount collection of ~6,600 mounts was built by Stephen and Janet Cares. It incorporates the collections of Gilbert George and Leland Wyman as well as many specimens supplied by the Cares. The micromount collections are rich in rare species and significantly supplement the collection of hand specimens.