Candida krusei is an opportunistic pathogen commonly implicated in urinary tract infections in immunocompromised patients. We present the first case of C. krusei renal cyst infection, occurring in a post-liver and kidney transplant patient with autosomal dominant polycystic kidney disease. Her persistent candiduria and fevers were refractory to prolonged therapy with AmBisome (Fujisawa Pharmaceuticals Co. Ltd., Osaka, Japan). She eventually required bilateral nephrectomies of her native kidneys. Cystic fluid was aspirated from six hemorrhagic and six nonhemorrhagic cysts. Cystic fluid cultures yielded C. krusei. Fluid from the nonhemorrhagic cysts was also analyzed for amphotericin B levels, measured using a bioassay. Free amphotericin B levels in the cysts were lower than the minimal inhibitory concentration for amphotericin B for this organism. We provide the first description of amphotericin B levels in cystic fluid obtained during bilateral nephrectomies.