Field-effect transistor (FET)-based biosensors exhibit excellent performance characteristics such as small size, ease of mass production, high versatility, and comparably low cost. In recent years, numerous FET biosensors based on various nanomaterials including silicon nanowires, carbon nanotubes, graphene, and transition metal dichalcogenides have been developed to detect a wide range of biomarkers that play a crucial role in early disease diagnosis, therapeutic monitoring and prognostic assessment. This review provides an overview of the structure, working principle, functionalization strategies and detection factors associated with FET biosensors based on diverse nanomaterials. Additionally, this paper discusses the applications of these diagnostic devices for detecting clinically relevant biomarkers such as nucleic acids, metabolites, proteins, cancer biomarkers, and hormones among others. The concluding section provides a comprehensive overview of the numerous challenges encountered in the widespread implementation of nanomaterial-based FET biosensors for clinical detection, while also presenting the future prospects for these biosensors based on current research advancements.