Nosocomial infections place a heavy burden on overstretched health services. An audit of junior doctors' sick leave behaviour was undertaken in 1993 and again in 2001. The object was to ascertain the level of common infectious illness and to investigate whether junior doctors were remaining at work inappropriately. The doctors were asked if any factors had influenced their decision to take sick leave or not. Between the two audits several initiatives have been introduced to improve the working conditions of junior doctors, including the New Deal to reduce hours of work. Eighty one junior doctors in a large teaching hospital participated in 1993 and 110 in 2001. The number reporting an infectious illness in the previous six months was similar (61.7% in 1993, 68.2% in 2001). There had been a significant increase in the percentage of infectious illness episodes for which the doctors took sick leave (15.1% in 1993, 36.8% in 2001, p < 0.001). The most common reason for taking less sick leave than was felt necessary was concern about colleagues having to do extra work (72% in 1993, 68% in 2001). Consultant pressure was cited by 26% (1993) and 20% (2001). Use of the staff occupational health unit was minimal, with none of the ill doctors contacting the department in 1993 and only three in 2001. Overall, despite the reduction in the number of infectious doctors not taking sick leave, the majority remained at work. Fundamental changes are needed if potentially infected doctors are not to present a risk of iatrogenic infection.