Interstitial nephritis caused by BK polyomavirus is an important complication of kidney transplantation. A diagnosis of BK virus nephropathy is established by a combination of characteristic histological, immunostaining, and ultrastructural findings. We report the first documented case of BK virus nephropathy caused by the KOM-3 strain in a patient after kidney transplantation. The biopsy specimen showed the characteristic histological and ultrastructural findings of BK virus, but was negative on immunostaining with a monoclonal antibody directed against BK virus large T antigen (LTag). Kidney tissue was subjected to polymerase chain reaction amplification using BK virus LTag-specific primers followed by DNA sequencing. Sequence results showed 100% homology to the KOM-3 strain, which has a 4-amino acid deletion in the C terminus of LTag compared with the reference sequence DUN strain. This deletion can explain the negative immunostaining results because the monoclonal antibody is directed against an epitope in this region. The patient lost his graft 2 months after diagnosis. Pathologists should be aware of this potential pitfall in interpreting immunostaining for BK virus. The incidence and prognostic implications of KOM-3 strain require additional studies.