Immunohistochemistry is increasingly utilized to differentiate lung adenocarcinoma and squamous cell carcinoma. However, detailed analysis of coexpression profiles of commonly used markers in large series of whole-tissue sections is lacking. Furthermore, the optimal diagnostic algorithm, particularly the minimalmarker combination, is not firmly established. We therefore studied whole-tissue sections of resected adenocarcinoma and squamous cell carcinoma (n ¼ 315) with markers commonly used to identify adenocarcinoma (TTF-1) and squamous cell carcinoma (p63, CK5/6, 34bE12), and prospectively validated the devised algorithm in morphologically unclassifiable small biopsy/cytology specimens (n ¼ 38). Analysis of whole-tissue sections showed that squamous cell carcinoma had a highly consistent immunoprofile (TTF-1-negative and p63/CK5/6/34bE12-diffuse) with only rare variation. In contrast, adenocarcinoma showed significant immunoheterogenetity for all 'squamous markers' (p63 (32%), CK5/6 (18%), 34bE12 (82%)) and TTF-1 (89%). As a single marker, only diffuse TTF-1 was specific for adenocarcinoma whereas none of the 'squamous markers,' even if diffuse, were entirely specific for squamous cell carcinoma. In contrast, coexpression profiles of TTF-1/p63 had only minimal overlap between adenocarcinoma and squamous cell carcinoma, and there was no overlap if CK5/6 was added as a third marker. An algorithm was devised in which TTF-1/p63 were used as the first-line panel, and CK5/6 was added for rare indeterminate cases. Prospective validation of this algorithm in small specimens showed 100% accuracy of adenocarcinoma vs squamous cell carcinoma prediction as determined by subsequent resection. In conclusion, although reactivity for 'squamous markers' is common in lung adenocarcinoma, a two-marker panel of TTF-1/p63 is sufficient for subtyping of the majority of tumors as adenocarcinomas vs squamous cell carcinoma, and addition of CK5/6 is needed in only a small subset of cases. This simple algorithm achieves excellent accuracy in small specimens while conserving the tissue for potential predictive marker testing, which is now an essential consideration in advanced lung cancer specimens. Modern Pathology (2011Pathology ( ) 24, 1348Pathology ( -1359 doi:10.1038/modpathol.2011; published online 27 May 2011Keywords: adenocarcinoma; CK5/6; p63; squamous cell carcinoma; TTF-1; 34bE12Adenocarcinoma and squamous cell carcinoma are the two major subtypes of non-small cell lung carcinoma. Until recently, therapeutic approaches to non-small cell lung carcinoma were largely guided by tumor stage, and there was no difference in treatment for adenocarcinoma vs squamous cell carcinoma. This monolithic approach to non-small cell lung carcinoma has dramatically changed in the last few years as a result of three major advances in thoracic medical oncology for advanced disease. These include (1) EGFR-targeted therapies, erlotinib