Infections are a frequent consequence of natural disasters. Repatriated victims may require hospital care due to multiple fractures, pneumonia or wound infections caused by multi-resistant pathogens that require specific infection control measures. To address potential pitfalls of infection control and clinical care in repatriated patients, we sought to provide microbiological insight into the possible origins of multi-drug antibiotic resistance in survivors of natural disasters. A review of the medical literature was performed from 1986 to 2006 with an emphasis on the 2004 tsunami disaster in the Indian Ocean. After natural disasters, polymicrobial infections may occur following heavy inoculation during trauma. Multi-resistant Gram-negative pathogens are more prevalent than Gram-positive bacteria. A high incidence of extended spectrum beta-lactamase-producing bacteria and difficult-to-treat fungal infections in otherwise immunocompetent hosts may challenge routine hospital care. We recommend that survivors of natural disasters should be kept in pre-emptive contact isolation during air transport and hospitalisation until the results of all microbiological cultures become available. A meticulous diagnostic work-up is necessary upon admission and empiric antibiotic treatment should be avoided. Infections may also become manifest after several weeks of hospitalisation. In case of life-threatening infection, antibiotic therapy should cover non-fermenting pathogens.