In this study, samples from multifocal renal tumors from two dogs affected with renal cystadenocarcinoma and nodular dermatofibrosis (RCND) were collected for detection of putative second hits in the FLCN gene. Genomic DNA from the samples was typed at the previously identified disease-associated missense mutation and cDNA representing the entire coding region of the FLCN gene was sequenced for mutation detection. Second hits with predicted functional implications for the wild-type FLCN allele were observed in 12 of 17 (71%) of the kidney tumor samples. The type of mutation of the second hits varied between the tumors. Different alternative splice mutations were detected, as well as loss of heterozygosity at the germline mutation and loss of transcription product of the wild-type FLCN allele. In total, the frequency and wide spectrum of second hits identified in the tumor samples suggests a tumor suppressor function of FLCN in the kidneys of RCND-affected dogs. No mutations were detected in skin nodules sampled from the two dogs. This shows that the skin tumors of RCND-affected dogs may be caused by haploinsufficiency of the FLCN gene product.