A method of treating a patient with a pulmonary disease, where the method includes delivering a dose of aerosolized medicament intermittently to a ventilator circuit coupled to the respiratory system of the patient. Also, a method of treating a patient with a pulmonary disease, where the method includes taking the patient off a ventilator, and administering to the patient, a nebulized aerosol comprising from about 100 μg to about 500 mg of a medicament. Also a method of treating a patient with a pulmonary disease, the method comprising administering an aerosolized first medicament comprising amikacin to the patient and administering, systemically a second medicament comprising an antibiotic to the patient that also treats the pulmonary disease, wherein a resulting amikacin concentration in the lung and/or pulmonary system is therapeutically-effective, and an amount of the systemically administered antibiotics is reduced.