Many refugees arriving in Germany originate or have travelled through countries with high prevalence of multidrug-resistant Gram-negative organisms. Therefore, all unaccompanied refugee minors (<18 years-old) arriving in Frankfurt am Main between 12 October and 6 November 2015, were screened for multidrug-resistant Enterobacteriaceae in stool samples. Enterobacteriaceae with extended spectrum beta-lactamases (ESBL) were detected in 42 of 119 (35%) individuals, including nine with additional resistance to fluoroquinolones (8% of total screened), thus exceeding the prevalences in the German population by far.