- The Roman Period Collection
- The Prehistoric Archaeology Collection
- The Medieval Archaeology Collection
- The Guilds Collection
- The Collection of Objects of Piety
- Militaria
- The Collection of Decorations
- The Collection of Plaques, Medals and Badges
- The Collection of Paintings, Graphics and Applied Graphics
- The Collection of Photographs, Photographic Equipment and Postcards
- The Collection of Architectural Documentation
- Zagreb in Homeland War Collection
- The Collection of Ivan pl. Zajc
- The Collection of Margita and Rudolf Matz
- Donation to the City of Zagreb: The Dr Ivan Ribar and Cata Dujšin-Ribar Memorial Collection
- Donation to the City of Zagreb: The Miroslav and Bela Krleža Memorial Space
- Donation to the City of Zagreb: The Collection of Mechanical Music Automata of Ivan Gerersdorfer
- Donation to the City of Zagreb: The Collection and Flat of the Architect Viktor Kovačić
- Donation to the City of Zagreb: Dr Ante Rodin's Collection of Old Packaging
- Donation to the City of Zagreb: The Collection of Tilla Durieux
- The Memorial Centre of the Rocket Attacks on Zagreb 1991/1995
