The complete sequence of the genome of bovine polyomavirus (BPyV), formerly known as the CK isolate of the stump-tailed macaque virus, is presented. The genomic organization of BPyV is similar to that of the non-rodent polyomaviruses. With a genome size of 4697 bp, BPyV has the smallest polyomavirus genome known so far. When compared to simian virus 40 (SV40), the shortness of the BPyV genome is due mainly to differences in the coding capacity of the BPyV early region. The first exon of the proposed large T antigen encodes only 35 amino acids; also, a coding region corresponding to the C-terminal 64 amino acids of the SV40 large T antigen is absent in BPyV. It is proposed that the nucleotide sequence encompassing the small t antigen coding sequence contains an intron sequence of 71 nucleotides. Together the two exon sequences encode a 124 amino acid protein. We conclude that this may be the first example of a polyomavirus that has a small t antigen which is translated from two exon sequences. The enhancer region of BPyV does not show homology to the SV40 enhancer sequences. An agnogene is present with a coding capacity of 118 amino acid residues. The highest degree of homology to SV40 and PyV is present in the VP1 molecule.