In the past years sprouting seeds have been linked to several foodborne outbreaks. An additional food safety concern is the potential role of produce as carriers of antibiotic resistant bacteria. This study evaluated the presence of foodborne pathogens and extended spectrum β-lactamases (ESBL)-producing bacteria in 102 sprout samples collected from the Swiss market. Salmonella, Shigatoxin-producing E. coli and Listeria monocytogenes were not detected but 3 samples were positive for ESBL-producing Enterobacteriaceae (Klebsiella variicola, Enterobacter cloacae, E. coli). The seeds and sprouts of those 3 positive samples originated from Switzerland. The Klebsiella variicola and Escherichia coli isolate harbored the clinically important blaCTX-M-14 gene, whereas blaCTX-M-3 was present in the Enterobacter cloacae isolate. Although these results assert an overall favorable situation in terms of the occurrence of foodborne pathogens in sprouting seeds in Switzerland, these products constitute a possible route for the spread of ESBL-producing Enterobacteriaceae, which constitutes a food safety issue.