Quantum dots (QDs) are semiconductor materials that have gained great interest due to their unique characteristics like optical properties. They are extensively being used in different areas, including solar cells, light-emitting diodes, laser technology, as well as biological and biomedical applications. In this review, comprehensive information about different aspects of QDs is provided, including their types and classifications, synthesis approaches, in vitro and in vivo toxicity, biological applications, and potentials in clinical applications. With a focus on the biological aspects, the respective in vitro and in vivo studies are collected and presented. Various surface modifications on QDs are discussed as directly influencing their properties like toxicity and optical abilities. Given the promising results, these materials are clinically used for targeted molecular therapy and imaging. However, there are a large number of questions that should be addressed before the wide application of QDs in a clinical setting. Regarding the existing barriers to QDs, suggestions are given and discussed to present an appropriate route for the clinical use of these materials.