Although abdominal surgery is an established risk factor for invasive candidiasis, the precise role of antifungal prophylaxis in these patients is not agreed upon. In 2007, fluconazole was added to the prophylactic antibiotic treatment for patients with gastrointestinal tract perforations or reoperation after colorectal surgery in two university hospitals in Copenhagen. Changes in candidaemia rates associated with this intervention were examined and potential interfering factors evaluated. Rates and clinical characteristics of candidaemias and other blood stream infections (BSIs) in abdominal surgery patients were compared before (1 January 2006 to 30 June 2007) and after the intervention (1 January 2008 to 30 June 2009). The departments' activity was assessed by number of bed-days, admissions and surgical procedures, and the consumption of antifungals was analysed. The candidaemia rate decreased from 1.5/1000 admissions in the pre-intervention to 0.3/1000 admissions in the post-intervention period (p 0.002). Numbers of BSIs and bed-days remained stable, and numbers of admissions and surgical procedures performed increased during the study period. Fluconazole consumption in the two abdominal surgery departments increased from 4.6 to 12.2 defined daily doses per 100 bed-days (p<0.001), and 3.2 to 5.0 (p 0.01), respectively, but remained unchanged in the intensive care units. We could not detect any increase in fluconazole-resistant strains (14/29 pre- and 2/7 post-intervention, p 0.43). The introduction of fluconazole prophylaxis was followed by a significantly decreased candidaemia rate. However, the observational study design does not allow conclusions regarding causality. No increase in resistance was detected, but follow-up was short and continuing surveillance is needed.