Can Escherichia coli be used as an indicator organism for transmission events in hospitals? Perineal and pharyngeal swabs were obtained from patients admitted to a medical or surgical intensive care unit within 24 h of admission and then twice per week. Escherichia coli isolates were typed by random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) typing. Based on the typing results, transmission rates for RAPD and AFLP typing were 8.5 and 6.6 per 100 patient-days. Requiring in addition to similarity in genotype parity in time and place for a transmission event, the incidence dropped to 3.8 (RAPD) and 1.7 (AFLP) per 100 patient-days. The two typing methods not only differed with respect to numbers of transmissions identified, but also to individuals involved in transmissions. This study identified a number of problems regarding the use of Escherichia coli as indicator organism for transmission events. The use of Escherichia coli for this purpose cannot be recommended at the moment.