The Croatian Institute for Brain Research (CIBR) is the largest research unit of the Zagreb School of Medicine, which has been conducting research in the program entitled Neurobiology of Cognitive Development and Cognitive Disorders since 1997. This program currently encompasses 28 individual (intramural as well as extramural) projects in basic and clinical neuroscience, thus representing the single largest program in Croatia. Another program  at the CIBR is related to the Pathophysiology of the Cerebrospinal Fluid. During the past six years, researchers at the CIBR published over 100 papers in high-profile international journals, with a focus on human developmental neurobiology, pediatric neuroimaging, and the biological basis and pharmacogenomics of mental and neurological disorders.

Over the past decade, the Department of Neurosurgery (in collaboration with the Croatian Institute for Brain Research, the Center for Clinical Implementation of Neuroscience, the Department of Electroacoustics of the Faculty of Electrical Engineering and Computing in Zagreb, and the Institute of Naval Engineering in Zagreb) has performed  significant research on the use of high energy ultrasound on experimental animal neural tissue, and successfully constructed an endoscopic ultrasound contact probe for the use in neurosurgery (so far used in clinical work for third ventriculostomy and endoscopic surgery of third ventricle tumors, with a prospect for application in other fields of endoscopic surgery, such as urology, ENT, and orthopedics).