The answer depends on context: If you are interested in resolution of injury in an experimental model system then you probably want to assess lung structure (histology).

If you are interested in phenotyping humans then I would look for some measure of lung function such as lung volumes, measures of gas exchange (P/F & Vd/Vt) and radiologic resolution of infiltrates.

Hi Rolf, we've been starting to look at histology which is great for measuring injury, but it is harder to look at resolution this way. We have the ability to measure physiological lung function in mice but these experiments are terminal so longitudonal study of a mouse isn't possible. I've been doing flow cytometric analysis of BAL fluid and long homogenate, and am looking for soluble markers that indicate resolution in the BAL such as IL-1RA, IL-10 etc but these are tricky as they're part of such a dynamic process. 

I appreciate your problem. I am not a cytokine expert, but it is my impression that we lack reference data (in humans or animals) on the temporal corrlations between specific cytokine profiles and measures of lung structure or function during the repair process.