Culture-dependent detection of gastroenteric bacteria is labour-intensive and does not provide results in a clinically relevant time frame. Several commercially available multiplex molecular panels are now available which may be more sensitive and could potentially provide rapid results. We compared the diagnostic accuracy, turnaround time and ease of use of three such molecular panels: the RIDA®GENE Bacterial Stool and EHEC/EPEC Panels (R-Biopharm AG, Darmstadt, Germany), the FTD® Bacterial Gastroenteritis Panel (Fast Track Diagnostics, Junglinster, Luxembourg) and the BD MAX™ Enteric Bacterial Panel (Becton Dickinson GmbH, Heidelberg, Germany). The results from 116 retrospective selected and 318 prospective unselected stool samples were compared with conventional culture-based techniques using a gold standard for a positive test of either culture or agreement in two of the three molecular panels. For most targets, the molecular panels were more sensitive than culture, detecting an additional 13 cases that culture missed. The laboratory turnaround time was under 3 h for all molecular panels, compared with 66.5 h for culture. The BD MAX™ panel was the fastest, easiest to use and most flexible.