Drs. Mukhopadhyay and Gal have written an excellent review of granulomatous lung disease in the May 2010 issue of Archives of Pathology and Laboratory Medicine, which has a "Special Section" featuring non-neoplastic lung disease.
One of their points, that cannot be emphasized enough IMHO, is the crucial importance of trying to identify an organism since infection is the most common cause of pulmonary granulomas. This is tedious work and requires a certain grim determination. It often feels like trying to "find a needle in a haystack." But I can also say that it is very rewarding to identify an organism so that proper therapy can be administered to the patient. Re-emphasizing a point made by Ulbright and Katzenstein (1980), examination of additional blocks or sections showing necrosis with special stains is indicated when the histologic appearance suggests infection. The authors also provide some helpful guidance in reporting situations when the stains are still negative.
Another very helpful item is in Table 2. which lists key diagnostic features of major non-infectious causes of granulomatous inflammation in the lung. Keep this in your vade mecum.
Keep in mind the distribution of the granulomas. I find this to be very helpful in generating a differential diagnosis, especially when special stains for organisms are negative. The authors nicely reiterate this point.
Another important point is to be aware of PCR and other immunohistochemical and molecular methods for identifying organisms in FFPE tissue, especially for suspected mycobacterial infection. It is worth considering ordering these additional tests when tissue was not obtained for culture or when mycobacterial infection is suspected clinically but routine ZN stains are negative.
The descriptions of the various major non-infectious entities associated with pulmonary granulomatous disease are as good as found in the major specialty textbooks and are a great reference. I mean, 196 references, are you serious?!