Conventional microbiological methods for bacterial enteric disease diagnosis are time-consuming, labour intensive and provide low sensitivity. The aim of this study was to evaluate the results of a new diagnosis strategy which replaces traditional stool culture with a molecular detection using the BD MAX™ System (BD Life Sciences, Sparks, Maryland, United States) as first-line assay together with reflective culture. A total of 1.590 specimens were prospectively requested for stool culture. The molecular detection included the BD MAX enteric bacterial panel together with the BD MAX extended enteric bacterial panel (BDM GIP) performed simultaneously on the same stool specimen. In 18.8% of specimens (176 of the 936 valid samples) there was one or more than one target positive with the following percent positivity: 9.7% Campylobacter spp., 5.7% Salmonella spp., 1.3% Shiga toxin genes (stx1/stx2), 1.2% Shigella spp./enteroinvasive Escherichia coli (EIEC), 1% Yersinia enterocolitica, 1% Vibrio spp. (V. vulnificus/V. parahaemolyticus/V. cholerae), 0.3% Plesiomonas shigelloides, and 0.2% Enterotoxigenic E. coli (ETEC) enterotoxin LT/ST genes. Positive reflective stool culture noted a correlation of 69.5% with the molecular test, missing 23.9% and 15.4% in the cases of Campylobacter spp., and Salmonella spp., respectively. In conclusion, this clinical study demonstrated very good performance of the BDM GIP. The performance and ease of use may provide advantages to many laboratories, improving the detection of bacterial stool pathogens and time to reporting results.