A rapid and sensitive method was developed for analysis of α-amanitin, β-amanitin, and phalloidin by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this method, α-cyano-4-hydroxy cinnamic acid was used as the matrix to assist the ionization of toxins. The identification of α-amanitin, β-amanitin, and phalloidin was achieved through their sodium adducts [M+Na]+ at m/z = 941, 942, and 811, and quantification of the three toxins was also achieved using microcystin RR at m/z = 1038 as internal standard. For all toxins, the limit of detection was 5 ng/ml, and all calibration curves were linear in the range of 10–500 ng/ml using 0.4 ml of urine. The sensitivity for identification was increased about tenfold when the tandem MS (MS–MS) mode was used for detection. Because these quantifications could be achieved in the toxin concentration range of 4–200 ng, the present MALDI-TOF MS method can serve as the most sensitive method so far reported for the analysis of these mushroom toxins. To our knowledge, this study is the first trial to analyze amanitins and phalloidin by MALDI-TOF MS (-MS).