With high numbers of refugees arriving in Europe uncertainty exists as to whether multidrug-resistant organisms are imported into the healthcare system. In our study, we identified 383 refugee-inpatients admitted to the University Hospital Münster, Germany between September 2015 and September 2016. For this patient cohort screening for Methicillin-resistant Staphylococcus aureus (MRSA), multidrug-resistant Gram-negative bacteria (MDR-GNB) and Vancomycin-resistant enterococci (VRE) was recommended in our institution. Until May 2016 pre-emptive isolation was applied to all refugee-inpatients until the exclusion of these multidrug-resistant organisms. MRSA were found in 34 refugee-patients (9.8%), MDR-GNB in 25 refugee-patients (12.9%) and VRE in none of the refugee patients. We did not find any strains carrying carbapenemases. Whole genome sequencing (WGS) data demonstrated that the respective isolates were genetically heterogeneous and revealed no transmission of refugee-patient isolates to other patients. We therefore omitted pre-emptive isolation as an infection control measure for this group of patients. Furthermore, molecular typing did not show evidence for nosocomial transmission from refugee-patients to other patients. Standard hygiene measures successfully prevented the transmission of refugee-patient isolates to other patients and as a result introduction into the healthcare system. This underlines that any multidrug-resistant organisms present within this cohort are not of any extraordinary concern for health systems.