Protozoal diseases are increasingly recognized as the cause of diarrhoeal outbreaks in both developed and developing countries. Cyclospora cayetanensis has been responsible for several epidemics in the last decade. In March 2005, an outbreak of diarrhoea was identified in recruits at the Ancon Naval Base in Lima, Peru. A case-control study was carried out. The overall diarrhoea attack rate was 53% (45/85). Complete data from 52 recruits were available for the analysis; 37 met the criteria for case and 15 for control. The epidemic curve indicated a point source transmission, with cases occurring over 9 days with a peak on the fifth day. Cyclospora cayetanensis was found in 7/37(18.9%) cases and 1/15 (6.7%) controls via standard microscopic techniques. PCR for C. cayetanensis detected 20/35 (57.1%) cases and 3/15 (20%) controls, demonstrating the improved diagnostic yield of this technique. This is the second report to characterize an outbreak of diarrhoea due to C. cayetanensis in Peru among a local population. The epidemiology and clinical course were similar to other reported outbreaks in developed regions. PCR greatly increased the number of C. cayetanensis cases detected during this outbreak, allowing the correct identification of its aetiology.