Despite nearly two decades since the discovery of gene fusions involving TFE3 or TFEB (“TFE”) in sporadic renal cell carcinoma (RCC), the molecular mechanisms underlying the renal-specific tumorigenesis remains largely unclear. The recent publication of the TCGA Network's clear cell kidney cancer paper provides further evidence for the importance of gene fusions by identifying 5 tumors harboring SFPQ-TFE3 fusions that otherwise lacked the common clear cell RCC associated mutation. Herein, we review key molecular features of TFE-fusion RCC, including candidate signaling pathways contributing to oncogenesis and a detailed overview of gene fusion isoforms based on an updated knowledge of TFE genetic organization. A total of 5 TFE3 gene fusions (PRCC-TFE3, ASPSCR1-TFE3, SFPQ-TFE3, NONO-TFE3, CLTC-TFE3) and 1 TFEB gene fusion (MALAT1-TFEB) have been identified in RCC tumors and characterized at the mRNA transcript level, with considerable heterogeneity in exon structure across different tumors, even for the same fusion partners. Common to all TFE3 and TFEB fusion isoforms is the retention of the wild-type protein C-terminus, including domains for DNA-binding, dimerization, and nuclear localization, but interestingly, not transcriptional activation. Despite this, the most widely accepted model explaining TFE-fusion oncogenesis remains the introduction of a constitutively active promoter leading to dysregulated TFE transcriptional activity. A multitude of molecular pathways well-implicated in carcinogenesis are regulated in part by TFE3 and/or TFEB protein, including activation of TGFβ and ETS transcription factors, E-cadherin expression, CD40L-dependent lymphocyte activation, mTORC1 signaling, insulin-dependent metabolism regulation, folliculin signaling, and Rb-dependent cell cycle arrest. Determining which pathways are most important will be critical to discovering the most promising therapeutic targets for this disease. Useful to this goal is a panel of cell lines derived from different TFE3-fusion RCC patient tumors, representing multiple fusion isoforms.