The invention provides oligonucleotides capable of inhibiting human papillomavirus (HPV) replication. More specifically, the invention provides oligonucleotides complementary to the translational start site of the HPV E1 open reading frame which inhibit HPV replication through interaction with a nucleic acid or a protein target. Oligonucleotides of the invention contain at least 4 deoxyribonucleotides and/or ribonucleotides and may include a variety of modifications to the internucleotide linkages or the mononucleotides. Furthermore, the invention provides pharmaceutical compositions and methods for treating disorders or diseases associated with HPV infection.