The pathogenesis of polyomavirus-associated interstitial nephropathy (PVAN) in kidney transplant recipients is likely to depend upon multiple risk factors, which may include viral characteristics. We report a case of interstitial nephropathy in a young kidney allograft recipient, associated with a BK virus (BKV) strain with a rearranged transcription control region (TCR). BKV strains with deletions and nucleotide substitutions in the TCR were present in a kidney biopsy and urine samples. After retransplantation, following loss of renal function, a BKV strain with an archetypal TCR was detected in association with asymptomatic reactivation.