In this study, we analyzed the BK polyomavirus (BKPyV) genome derived from three rodent cell lines established from tumors that were experimentally induced by injecting BKPyV into newborn rodents. Three cell lines (Vn-324, In-1024, and Vn1919) were recently deposited in the JCRB Cell Bank. Vn-324 was established from a hamster choroid plexus papilloma induced by injecting purified BKPyV Gardner strain wild-type 501 ( wt-501) into new born hamster. This cell line was reported to be negative for the large T-antigen using indirect immunofluorescence. In this study, we examined the large T-antigen expression using the reverse-transcriptase-polymerase chain reaction (RT-PCR). Vn1919 was established from a mouse ependymoma induced by the injection of purified plaque morphology mutant 522 ( pm-522) into newborn BALB/c mice. In-1024 cells were established from hamster insulinoma, however, there have been no reports on the establishment of this cell line. The non-coding control region (NCCR) of BKPyV derived from Vn-324 genomic DNA and wt-501 had the same structure, whereas the NCCR of BKPyV derived Vn1919 genomic DNA and pm-522 had the same structure. BKPyV derived from In-1024 genomic DNA had a large deletion in the viral proteins 1, 2 and 3 (VP1, VP2, and VP3) coding region. Additionally, the structure of the NCCR had a different pattern from that of mutant variants pm-522 and wt-501. Our findings suggest that the hamster insulinoma, from which the In-1024 cell line was established, was induced by injecting a virus stock containing a proliferation-defective mutant variant that was expanded in human embryonic kidney cells.