In Switzerland, the first case of bovine spongiform encephalopathy (BSE) was diagnosed in November 1990. Case numbers peaked in 1995, with a total of 352 BSE cases identified by 30 April 2000. Reporting of clinically suspect cattle is currently the most commonly used method world-wide to detect BSE cases. The effectiveness of mandatory reporting depends on a variety of factors; for other diseases passive surveillance underestimates the incidence of clinical cases. The efficiency of passive surveillance systems for BSE will remain unknown until screening tests able to identify clinically affected cattle have been applied in several countries. This paper provides the first detailed description of a targeted screening programme for BSE. Two populations of cows >24 months of age were included in the targeted screening: (i) cows found dead or culled on site where the carcass was submitted to rendering (fallen stock) and (ii) cows with health-related problems unfit for routine slaughter that were slaughtered under emergency procedures (emergency slaughter). Between 1992 and 1999, on average 81 clinical BSE suspects per year were reported to the veterinary authorities (passive surveillance), of which 43% were confirmed with BSE. A total of 30 clinical cases were captured by passive surveillance and an additional 20 BSE cases detected by targeted screening between May 1999 and April 2000. The odds of finding a BSE case was 49 times higher in the fallen stock and 58 times higher in emergency-slaughtered cattle when compared to passive surveillance. The targeted screening of fallen stock and emergency-slaughtered cattle considerably increased the number of detected cases in this 12-month period. Targeted-screening cases were on average 4 months younger than the clinical suspect cases. In conclusion, post-mortem testing of fallen stock and emergency-slaughtered cows >24 months for BSE is an important active surveillance element within a total surveillance system that principally is based on mandatory reporting of clinical suspect cases. Without ante-mortem screening tests to detect BSE-infected cattle during the incubation period, a combination of effectively functioning passive and active BSE surveillance strategies might be the only approach to assess the BSE situation reliably in a given country or region - and it is necessary to substantiate claims of freedom from the disease.