The Department of Physics established the following Divisions: Experimental Physics Division, Division of Theoretical Condensed Matter Physics, Theoretical Physics Division of Particles and Fields, and the Division of Theoretical Physics. Additionally was established a Center for technical support to the Department of Physics.

Experimental Physics Division has particular interest in experimental solid state physics, atomic and molecular physics, nuclear physics, and physics of medium and high energy, astrophysics, biophysics and methodology of educational physics.
The Experimental Physics Division is home to highly-advanced research. Members of the Division are successful supervisors and leaders of international and national competitive projects.

There are a dozen advanced research laboratories for investigations in low temperature physics, high magentic fields, solid state NMR and high frequency measurements, microstructural research, synthesis and measurement of transport, magnetic and thermodinamic properites, nuclear physics, intermediate and high energies, optical spectroscopy, investigation of magnetic and electrical phenomena and observational astrophysics.

Theoretical Physics Division  is Croatia's flagship research center in the field of theoretical physics, in particular in atomic and nuclear physics, optics and photonics, physics of condensed matter, and biophysics. Members of the Division  publish their frontier research work in leading international scientific journals and lead a number of competitive research projects and agreements on international scientific cooperation.

Theoretical Physics Division of Particles and Fields covers research subjects Gravitation and black holes and Phenomenology of elementary particles and fields. Research projects are Graparion - Gravity and parity violation and MIAU - Matter and Interactions at Accelerators and in Universe.

Theoretical Physics Division of Condensed Matter covers theoretical investigations that are focussed on the understanding of behavior of high-temperature superconductors in the same three groups of measurements, and on the elucidation of the mechanism of high-temperature superconductivity. Electronic and optical properties of artificially fabricated systems of low dimensionality and nanoscopic size are also under investigation.