Two cows from different herds in a district of Switzerland known to harbour ixodid ticks had erythematous lesions on the hairless skin of the udder, were in poor general condition with a poor appetite and decreased milk production, and had a stiff gait and swollen joints. Borrelia burgdorferi sensu strictu DNA was detected in samples of synovial fluid and milk from one of the cows and Borrelia afzelii DNA was detected in synovial fluid from the other by means of a real-time PCR.