Aims Need for accurate histologic subtyping of non-small cell lung carcinomas ( NSCLCs) is growing. IHC patterns may be ambiguous in some cases, rendering it difficult to determine subtypes. Methods and results Tissue microarrays composed of 184 resected NSCLCs were stained for TTF-1, Napsin A, CK7, p40, p63, CK5/6, and mucicarmine. TTF-1 and Napsin A were chosen as the most accurate adenocarcinoma ( ADC) marker ( ACM), and p40 as squamous cell carcinoma ( SCC) marker ( SCM). We then prospectively performed IHC using these markers ( TTF-1, Napsin A, and p40) in a cohort of small NSCLC biopsies ( n = 186) with ambiguous morphology. Of these biopsies, 82.8% (154/186) were classifiable into either ADC or SCC by applying '3-marker IHC panel'. Additional CK7, p63, and CK5/6 were applied in 30 biopsies with equivocal IHC patterns, including 18 ACM−/ SCM− (double-negative) and 12 ACM+/ SCM+ (double-positive) cases. Decision tree and support vector machine models revealed that TTF-1 was a critical single marker for ADC in double-positive cases (91.7% accuracy), whereas p63 and/or CK5/6 helped to subtype double-negative cases (72.2% accuracy). Conclusions We propose a novel comprehensive algorithm for subtyping NSCLCs using a 3-marker IHC panel and additional p63 and CK5/6 that would be useful for subtyping small NSCLC biopsies.