While a limited number of studies have investigated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in medical rehabilitation institutions, almost no data on the colonization of rehabilitation patients with multiresistant gram-negative rods is available. Here we report on a large multicenter study on the prevalence of MRSA and multiresistant pathogens in rehabilitation institutions in the Rhine-Main area in 2014. Altogether, 21 rehabilitation hospitals participated. For all patients, age, gender, previous history of hospitalizations, surgery, previous colonization with multidrug-resistant organisms, use of a medical device, current antimicrobial therapy, and the current infection status were ascertained. On voluntary basis, nare and throat swabs were taken for analysis of MRSA and rectal swabs were tested for extended spectrum betalactamase-producing gram-negative bacteria (ESBL). 50% of 2 440 patients had a history of hospitalization within the previous 6 months while 39% had undergone surgery during the past 30 days. Approximately a quarter of the patients had been transferred to a rehabilitation hospital directly from an acute care hospital, had been under antimicrobial therapy with the past three months, or had travelled to a foreign country within the previous year. Risk factors such as lesions of the intact skin or presence of medical devices were rarely reported (< 5%) within the exception of patients undergoing geriatric or neurologic acute care rehabilitation. 0.7% (15/2155) of the patients were colonized with MRSA, while 7.7% (110/1434) showed a positive result for ESBL. The highest prevalence rates for multiresistant organisms were encountered among patients with neurologic rehabilitation (MRSA, 1.3%, and ESBL, 10.2%) or with geriatric rehabilitation (MRSA, 9.4%, and ESBL, 22.7%). In the rehabilitation patient population, the prevalence rates of MRSA and ESBL were found to be in the range of rates encountered in the general population (reported rates for MRSA, 0.5%, and ESBL, 6.3%). The known risk factors for MRSA such as skin lesions, medical devices and previous history for MRSA were also confirmed among this patient population. Direct transfer from an acute care hospital, antimicrobial treatment during the past 3 months, and wounds proved significant risk factors for ESBL colonization. Patients of neurologic rehabilitation and geriatric patients showed the highest rates of risk factors and the highest prevalence rates of multidrug-resistant organisms. It appears to be of importance for rehabilitation hospitals to be geared to the needs of patients with multidrug-resistant organisms, and prevent the transmission of these pathogens by appropriate hygiene measures.