Methods and systems for isolating, assessing and treating lung compartments are disclosed. One or more lung compartments are accessed through an isolation catheter, oxygen rich gas is delivered to the compartments, and blood oxygen or exhaled carbon dioxide are monitored to assess lung compartment function. Diseased lung compartments may be treated using therapeutic agents delivered to the diseased compartments through the isolation catheter. Therapeutic agents include carbon monoxide, radioactive agents, chemotherapeutic agents or angiogenesis inhibitors and angiocidal agents.
