Among cases of polycystic kidney disease (PKD) complicated with tuberous sclerosis (TSC) (TSC-PKD), there have been advancements in gene analysis for TSC2/ PKD1 contiguous gene syndrome with poor renal prognosis. However, there are many unclear points about cases of TSC-PKD without PKD gene abnormalities. We here report a case of a 13-year-old girl who was found to have bilateral PKD while screening for TSC complications. Since TSC2/ PKD1 contiguous gene syndrome was suspected, genetic testing was performed. However, there were no abnormalities in the TSC2 gene, PKD1 gene or even in the PKD2 gene, despite the presence of TSC-PKD with prominent cysts. This result suggests that factors other than abnormalities in the PKD1 and PKD2 genes may be involved in the onset of PKD. Accumulation and analysis of TSC-PKD cases without PKD gene abnormalities are necessary for further elucidation of the pathophysiology of TSC-PKD.