Dr. McDonald subsequently practiced pulmonary and critical care in Portsmouth NH, where he was the medical director of the pulmonary physiology laboratory and respiratory services department.
He then moved to the Bay Area, where he worked in pulmonary and critical care at the Kaiser Oakland facility. He then moved to San Francisco, where he continued his practice in pulmonary and critical care. He was also the medical director of the pulmonary physiology laboratory in both facilities.
Dr. McDonald was the founder and director of the Asthma Center in San Francisco. He was the first physician in San Francisco to offer endobronchial ultrasound biopsies for the diagnosis of pulmonary diseases.
He currently has a referral practice in pulmonary medicine in San Francisco and is a consultant in occupational lung disease.
Dr. McDonald has provided service as the medical director for the Nomads Medical Mission in Nepal beginning in 2014, offering basic medical care to the most remote regions of the Himalayas. He has recently been involved with indigenous communities in South Dakota, helping establish an emergency medical service in the Lakota Nation.