Renal cell carcinoma (RCC) comprises five major molecular and histological subtypes. The Birt-Hogg-Dubé (BHD) syndrome is a hereditary human cancer syndrome that predisposes affected individuals to develop renal carcinoma of nearly all subtypes, in addition to benign fibrofolliculomas, pulmonary and renal cysts. BHD is caused by loss-of-function mutations in the FLCN protein. The molecular function of FLCN is still largely unknown; opposite and conflicting evidence of the role of FLCN in mTOR signaling/phospho-S6 (p-S6) activation have recently been reported. Here, we describe the expression pattern of murine Flcn and observe that homozygous disruption of Flcn results in embryonic lethality early during development. Importantly, heterozygous animals manifest early preneoplastic kidney lesions devoid of Flcn expression that progress toward malignancy including cystopapillary adenomas. Bona fide tumor suppressor activity of FLCN was confirmed by nude mouse xenograft assays of two human RCC cell lines with either diminished or re-expressed FLCN. Strikingly, tumor suppression by FLCN was independent of the status of another renal tumor suppressor, the von Hippel-Lindau gene (VHL). We observed that loss of FLCN expression leads to repression or stimulation of S6 activation in a context dependent manner. Indeed, solid tumors and normal kidney show decreased p-S6 upon diminished FLCN expression. Conversely, p-S6 is found to be elevated or absent in FLCN negative renal cysts. In accordance with clinical data showing distinct renal malignancies arising in BHD patients, this study demonstrates that FLCN is a general tumor suppressor in the kidney which operates on a unique and VHL-independent pathway.