All the human and animal laboratory reports of zoonoses sent to Health Protection Scotland between 1993 and 2002 were identified. There were 24,946 reports from veterinary laboratories, and 94,718 (20 per cent) of the 468,214 reports from medical laboratories were considered to be zoonotic. The most common reports of zoonoses from people were Campylobacter, Salmonella, Cryptosporidium and Giardia species and Escherichia coli O157. The most common reports of zoonoses from animals were Salmonella, Cryptosporidium, Chlamydia and Campylobacter species and Mycobacterium avium paratuberculosis. For all the zoonoses in people, the National Health Service Board areas Borders, Dumfries and Galloway, Forth Valley, Grampian, Lanarkshire and Lothian had a higher than expected standardised incidence rate of infection, whereas Ayrshire and Arran, Fife, Greater Glasgow, Shetland, Tayside and Western Isles had a lower than expected rate. The organisms and diseases considered to be new and emerging were Rhodococcus species, Cyclospora cayetanensis, Leishmania species, Pneumocystis carinii (jiroveci) and bovine spongiform encephalopathy/variant Creutzfeldt-Jakob disease.