BK virus (BKV), a virus belonging to the polyomavirus family, is a circular double-stranded DNA virus that causes nephropathies in immunocompromised patients after kidney or bone marrow transplantation. The occurrence of polyomavirus-associated nephropathy in kidney transplant patients may trigger graft loss, and guidelines for the management of BKV infection have not yet been clearly established. Treatment of BKV nephropathy with cidofovir (CDV) {(S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (HPMPC)}, an acyclic phosphonate analogue of dCMP with a broad antiviral activity against DNA virus infections, has been proposed. The benefit of this small-molecule-based treatment has been evaluated only with a limited number of cases. In this study, we report the evaluation of three different classes of acyclic nucleoside phosphonates for their activities against BKV replication in two different primary renal cells: renal proximal tubular epithelial cells (RPTECs) and human renal cortical epithelial (HRCE) cells. The data indicate that besides HPMPC and its cyclic form, (S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]-5-azacytosine (HPMP-5-azaC), cyclic HPMP (cHPMP)-5-azaC, hexadecyloxyethyl (HDE)-cHPMP-5-azaC, and 9-[2-(phosphonomethoxy)ethyl]guanine (PMEG) are the most selective inhibitors of BKV replication. On the contrary, leflunomide, which has also been proposed for the management of BKV-associated diseases, is not able to inhibit BKV replication at nontoxic concentrations