AIMS: The aim of this study was to determine whether endophytic Bacillus cereus isolates from agronomic crops possessed genes for the nonhaemolytic enterotoxin (Nhe) and haemolysin BL (HBL) and, therefore, have the potential to cause diarrhoeal illness in humans. METHODS AND RESULTS: PCR followed by sequencing confirmed the presence of enterotoxin genes nheA, nheB, nheC, hblA, hblC, hblD in endophytic B. cereus. All nhe genes were detected in 59% of endophytic B. cereus, while all hbl genes were detected in 44%. All six genes were detected in 41% of isolates. Enterotoxin genes were not detected in 15% of B. cereus isolates. Reverse transcriptase real-time PCR confirmed that endophytic B. cereus could express enterotoxin genes in pure culture. CONCLUSIONS: This study showed that endophytic B. cereus isolates that possess genes for enterotoxin production are present in agronomic crops. Other endophytic B. cereus isolates lacked specific genes or lacked all nhe and hbl genes. Additionally, host, country of origin and tissue of origin had no impact on the enterotoxin genes detected. SIGNIFICANCE AND IMPACT OF THE STUDY: Bacillus cereus with the potential of causing diarrhoeal illness in humans is a cosmopolitan endophytic inhabitant of plants, not incidental surface inhabitants or contaminants, as often suggested by previous research.