The application relates to the use of immunoregulatory polynucleotides and/or immunoregulatory compounds in combination with other therapeutic agents. The application further relates to immunoregulatory polynucleotides and/or immunoregulatory compounds comprising a modified immunoregulatory sequence. It also relates to the administration of the immunoregulatory polynucleotides and/or immunoregulatory compounds comprising a modified immunoregulatory sequence to regulate an immune response.