Introduction: Bacillus cereus is a human pathogen that causes two kinds of foodborne diseases, the emetic syndrome caused by emetic toxin or cereulide (Ces), and the diarrheal syndrome caused by three different enterotoxins, the hemolytic enterotoxin or hemolysin BL (Hbl), the nonhemolytic enterotoxin (Nhe) and the cytotoxin K (CytK). Objective: To determine the presence of toxigenic genes of Bacillus cereus in DNA samples directly obtained from corn starch and wheat flour using multiplex polymerase chain reaction. Material and methods: The presence of toxigenic genes of Bacillus cereus were determined in DNA samples directly extracted from corn starch and wheat flour, using a multiplex polymerase chain reaction technique specific for cesB, hblC, nheA and cytK genes. Results: From a total of 76 corn starch samples, 60.5% had toxigenic genes of Bacillus cereus and were grouped in six consortia: I: hblC, cytK (30.4%), II: nheA, hblC, cytK (21.7%), III: hblC (19.6%), IV: nheA (15.2%), V: nheA, hblC (10.9%) and VI: nheA, hblC, cytK, cesB (2.2%). From 79 wheat flour samples tested, 65.8% had toxigenic genes of Bacillus cereus and were grouped into four consortia: I: nheA, hblC, cytK (80.8%), II: hblC, cytK (11.5%), III: hblC (5.8%) and IV: nheA, hblC (1.9%). Conclusions: It was found that in corn starch the enterotoxigenic consortia predominated over the emetic while in wheat flour only enterotoxigenic consortia were detected. The study describes a multiplex polymerase chain reaction that allowed direct, rapid, and simultaneous detection of toxigenic genes of Bacillus cereus in foods.