PCR methods were developed for bovine polyomavirus detection in beef meat samples. BPyV-1 was detected in 1% of beef muscle samples from Germany. BPyV-1 and BPyV-2 were detected in 20–30% of ground beef samples from Germany. Genomes showed high sequence identities with BPyV-1 and BPyV-2a reference strains. Infectivity and tumorigenicity of the detected viruses remain to be investigated.