We set up a matched case-control study of potential risk factors for clinical encephalomyocarditis virus (EMCV) in 58 pig farms in West Flanders (Belgium). In total, 29 farms experienced a clinical outbreak of EMCV confirmed by EMC virus isolation. Mortality was seen only among suckling piglets (18 case farms), in piglets and other age-groups (4 case farms), or only among fattening pigs (7 case farms). Five farms had reproductive problems among the sows. Control farms were matched geographically on farm size and farm type and were selected on the absence of clinical signs. A questionnaire on potential risk factors for EMCV was developed to collect data at both case and control farms. The exploration of the data used clusters of factors associated with clinical EMCV infection: (a) rodents, (b) general farm set up and (c) general hygiene. The multivariable relationships between clinical appearance of EMCV and potential risk factors were tested with conditional logistic regression. The final model on all farms contained presence of mice (OR=8.3) as a risk factor for clinical EMCV infection while the flow of manure up through the slatted floor (OR=0.11) and movement of manure between manure pits in the pig stable (OR=0.14) were protective.