Methods for treating inflammatory pulmonary diseases by administering to the patient an effective amount of one or more pharmaceutical agents are disclosed. The pharmaceutical agents administered can include antibiotics, steroids, NSAIDs, DMARDs, growth factor receptor inhibitors, PI3K inhibitors, neurotransmitter receptor inhibitors, or protease inhibitors. The dose administered is effective to suppress or prevent initiation, progression, or relapses of disease, including the progression of established disease. The pharmaceutical agent is administered to a patient determined to have the disease and at an amount effective to suppress or prevent activity of the disease. The pharmaceutical agent is administered using a transtracheal, transbronchial, or transvascular drug delivery catheter. The pharmaceutical agent can be administered to the patients pulmonary tissue to suppress reactions in response to bronchial thermoplasty either before, during, or after bronchial thermoplasty.