Desmoplastic squamous cell carcinoma (DSCC) as a rare subtype of cutaneous SCC has specific histological features, characterized by columns, bands, and strands of squamoid cells infiltrating a dense collagenous stroma. To decrease the high rates of local recurrence in DSSC, improvement of diagnostic methods is highly demanded. Objective was to evaluate whether immunohistochemistry (IHC) is suited to increase diagnostic accuracy. A total number of 18 patients were included in this study. After recutting of the original paraffin blocks, parallel staining of serial sections with conventionally H&E and cytokeratin AE1/AE3-immunohistochemical staining was performed. Results were evaluated by an experienced dermatohistopathologist. In 55.6% (n = 10), the margins of 3D-histology still showed no evidence of neoplastic lesions in both stainings. In contrast, we found neoplastic lesions in 5 of 18 cases (27.8%) with cytokeratin AE1/AE3 staining, while H&E-staining remained negative. In addition, neoplastic lesions were found in both, H&E as well as cytokeratin AE1/AE3 staining in three cases (16.7%). The data presented show improvement of diagnosis in 27.8% of cases using IHC and 3D-histology. This method is suitable to improve the diagnosis of DSCC.