Recurrent gene fusions in cancers have been successfully applied in clinical diagnoses and treatments. Specific gene rearrangements or other specific cytogenetic translocations may be helpful in separating cancers from benign lesions. Also, the detection of gene fusions has brought great benefits to distinguish molecular subclassifications of cancers. Numerous approaches have been used to identify cancer-specific abnormalities, including FISH, RT-PCR, next-generation sequencing, etc. In addition to diagnostic and genetic values, molecular testing has been becoming a valuable tool in the therapeutic research. Recent clinical trials involving gene fusions in cancers have also been developing under a rapid speed. Generally, we review gene fusions in cancers, emphasizing on relevant diagnostic biomarkers, method selections, and treatments.