Brain organoids are specific three-dimensional cultures that by connecting cells form pieces of tissue and in that way imitate small parts of the brain. Since they consist of several types of cells organized in such a way as to mimic the cytoarchitecture of the brain in vivo, they represent the most faithful in vitro model of the brain. Brain organoids can be grown from embryonic stem cells and induced pluripotent stem cells, which can then be induced in several ways to differentiate into nervous system cells and form three-dimensional structures. Brain organoids have so far shown their potential in the research of developmental and neurodegenerative disorders of the brain, as well as tumors. They also have the capacity to discover and test new forms of therapy and drugs. Due to brain-like characteristics in vivo, such as three-dimensionality, composition of different cell types, and specific cytoarchitecture and microenvironment, brain organoids have many advantages over traditional two-dimensional cultures and animal models. At the same time, organoids have many disadvantages, such as the absence of vascularization, which limits their growth, and the insufficient development of cerebral gyri, which makes it difficult to research more complex diseases of the cerebral cortex. This thesis presents the advantages and possibilities of using brain organoids, as well as their disadvantages and limitations, with emphasis on studies on Zika virus infection, glioblastoma, Alzheimer's and Parkinson's disease.