Stenotrophomonas (Xanthomonas) maltophilia has recently emerged as an important nosocomial pathogen in immunocompromised cancer patients and transplant recipients. S. maltophilia has been documented as a cause of bacteraemia, infections of the respiratory and urinary tracts, meningitis, serious wound infections, mastoiditis, epididymitis, conjunctivitis and endocarditis. The reservoir of S. maltophilia and the mechanisms by which it is transmitted, remain largely unknown. Risk analysis has shown that mechanically ventilated intensive care unit patients, receiving antibiotics especially carbapenems, are at increased risk of colonization/infection. Because of the in vitro resistance to many commonly used agents, it is essential that S. maltophilia is isolated and identified correctly. Over the last decade Burkholderia (Pseudomonas) cepacia has become a major threat to the management of patients with cystic fibrosis (CF). The spread of B. cepacia through previously stable CF clinic populations, is an increasing cause for concern. Anxiety has arisen following the observation that some patients with previously mild disease, experience an accelerated and fatal deterioration in pulmonary function with fever, necrotizing pneumonia, and in some cases septicaemia. Early UK surveillance studies suggested a maximum prevalence of 7%, though this has risen in recent reports to approach the 40% described in the US. Mounting evidence of person-to-person transmission has led the Cystic Fibrosis Trust to issue guidelines for the management of colonized patients. In an attempt to monitor and understand the spread of B. cepacia, typing techniques such as ribotyping have been employed. Because of these problems, together with multiple-antibiotic resistance, there is an urgent need to identify the major routes of transmission, colonizing, pathophysiological and immunological factors.