Fumonisins are mycotoxins mainly produced by Fusarium verticillioides, which is a major contaminant of corn. However, there are sporadic reports of fumonisin contamination in wheat worldwide. The rice adherent fungus Gibberella fujikuroi is taxonomically closely related to F. verticillioides. Therefore, the potential risk of fumonisin contamination in rice and wheat is significant. Previously, a sensitive detection method utilizing liquid chromatography with tandem electrospray mass spectrometry (LC-ESI-MS-MS) was developed for the determination of fumonisins in brown rice. In the present study, the incidence of fumonisins in brown rice and wheat harvested in Japan was investigated using LC-ESI-MS-MS. Forty-eight rice samples and 47 wheat samples were screened and analyzed for the major B-type fumonisins: fumonisin B1 (FB1) and fumonisin B2 (FB2). About 1 kg of rice or wheat seed was divided into three subsamples, and 10 g from each subsample was used for the analysis. The limits of detection were 0.012 and 0.011 mg/kg for FBt and FB2, respectively, in rice samples and 0.010 and 0.008 mg/kg for FB1 and FB2, respectively, in wheat samples. The mean (standard deviation) recoveries of FB1 spiked at 0.50 mg/kg into toxin-free rice and wheat samples were 77.6 (4.2)% and 84.5 (3.1)%, respectively. One of the wheat samples was positive for FBt with a value greater than the limit of detection,but no fumonisin was found in any of the rice samples. This is the first report of fumonisins detected in Japanese wheat.