Cancer, one of the most life-threatening diseases, causes a heavy burden to both the society and family. Timely and efficient early diagnosis of cancer is critical to enable effective treatment and improving survival rate, which also is currently one of the most challenging problems in clinical medicine. Although modern medical imaging is an important tool for cancer diagnosis, detection of molecular biomarkers (such as DNA, RNA, proteins, and metabolites), released from the cancer cells or the organs, is the preferred approach for detecting and tracking cancer due to their unique association with genomic changes in cancer cells, especially for screening and early diagnosis of cancer. Molecular diagnosis can help doctors not only make a precise diagnosis in diseases’ early stage, but also make a judgment in disease staging, classification, curative effect monitoring and prognosis evaluation. A variety of conventional technologies are developed for biomarker detection, such as radio-immunoassay and enzyme-linked immunosorbent assay (ELISA), however, they are label-based, multi-step, time-consuming, and required experienced personnel to conduct the experiment. Silicon nanowire field-effect transistors (SiNW-FETs), as new one-dimensional semiconducting nanostructures, exhibit some unique properties, including high surface-to-volume ratios, fast electron transfer, and biocompatibility. SiNW-FET based biosensors have recently been attracted tremendous attention as a promising tool in biomedical and chemical detection because of their ultrasensitivity, specificity, label-free detection, and rapid and real-time response capabilities, which demonstrate a great potential in the application of medical diagnosis, chemical analysis, environmental monitoring, and food industry. Over the past decade, SiNW-FET biosensors are employed in the detections of DNA sequences, microRNAs, proteins, small molecules, cancer biomarkers, cells, and viruses. Here, we present a comprehensive review which introduces the working principle of SiNW-FETs, the fabrication of SiNWs, influence factors of the sensitivity, as well as the applications of SiNW-FET biosensors in cancers’ molecular diagnosis (including nucleic acid detection, biomarkers detection, and studies of molecule-molecule interactions). The future prospects in this area are also discussed, which can provide a guidance for the further applications in early diagnosis. SiNW-FET biosensors, as a promise tool in molecular diagnosis, held great potential applications in large-scale screening and point-of-care testing for early-stage cancer.