Reverse phase protein arrays (RPPA) have become an important tool for sensitive and highthroughput detection of proteins from minute amounts of lysates from cell lines and tissues preserved with liquid nitrogen. Since the current standard method for tissue preservation in almost all hospitals world-wide is formalin-fixation and paraffin-embedding (FFPE) it would be highly desirable if RPPA could also be applied to FFPE tissue. We investigated if the analysis of FFPE tissue lysates with RPPA would result in biological meaningful data in two independent studies. In the first study with breast cancer samples we assessed whether human epidermal growth factor receptor 2 (HER2) score based on immunohistochemistry (IHC) can be reproduced with RPPA. The results show a very good concordance between the IHC and RPPA classification of HER2. In the second study we profiled FFPE tumour specimens from patients with adenocarcinoma and squamous cell carcinoma in order to find new markers for differentiating these two subtypes of non-small cell lung cancer (NSCLC). The p21-activated kinase 2 (PAK2) could be identified as a new differentiation marker for squamous cell carcinoma. Overall, the results demonstrate the technical feasibility and the merits of RPPA for protein expression profiling in FFPE tissue lysates.