Migration is one of the risk factors for the spread of multidrug-resistant organisms (MDRO). The increasing influx of migrants challenges local health care systems. To provide evidence for both hospital hygiene measure and empirical antibiotic therapy, we analysed all cultures performed in asylum seekers between January 1st 2014 and December 31st 2015 for methicillin resistant Staphylococcus aureus (MRSA) and for multidrug-resistant Enterobacteriaceae (MDRE). We compared these with cultures from the Dutch patient population with risk factors for carriage of MDRO. A total of 7181 patients were screened for MRSA. 7357 S. aureus were isolated in clinical cultures. Of 898 screened asylum seekers, almost 10% were MRSA positive. Of 118 asylum seekers with S. aureus in clinical cultures almost 19% were MRSA positive. The general patient population had a 1.3% rate of MRSA in S. aureus isolates. A higher rate of Panton-Valentine leukocidin (PVL) positive strains (RR: 2.4; 95% CI: 1.6-3.4) was found in asylum seekers compared to the general patient population. In 33475 patients one or more Enterobacteriaceae were obtained. More than 21% of the asylum seekers were carrier of MDRE, most of them producing extended spectrum beta-lactamases (20.3%). 5.1% of the general patient population was MDRE carrier. It can be concluded that asylum seekers present with higher rate of MDRO compared to the general patient population. These results justify continued screening of asylum seekers to anticipate multidrug-resistant organisms during hospital care of patients.