3D cell cultures and organoid approach are increasingly being used for basic research and drug discovery of several diseases. Recent advances in these technologies, enabling research on tissue-like structures created in vitro is very important for the value of the data produced. Application of 3D cultures will not only contribute to advancing basic research, but also help to reduce animal usage in biomedical science. The 3D organoid approach is important for research on diseases where patient tissue is difficult to obtain. Therefore, this review aims to show recent advances in the 3D organoid technology in disease modeling and potential usage in translational and personalized medicine of diseases with limited patient material such as neurological diseases and rare diseases.