Squash smear cytology of Langerhans cell histiocytosis (LCH) has rarely been reported. We described squash cytological findings of cranial LCH. Additionally, based on recent data that suggests an association of LCH with either viral infection or genetic alteration, we investigated the presence of several viruses or mutation of TP53 and BRAF in LCH tissue samples. Intraoperative squash smears of a small tissue fragment excised from the lesion demonstrated a mixed population of eosinophils, neutrophils, small lymphocytes and a high content of histiocytes. The histiocytes possessed abundant dense cytoplasm with round cell shape and eccentrically located nuclei with fine chromatin, delicate nuclear membranes and prominent nuclear grooves, indentations and pseudoinclusions. The cytologic features were consistent with Langerhans cells (LCs). Subsequent histopathologic examination confirmed the diagnosis of LCH. Immunohistochemically, the LCs were positive for S-100, CD1a and langerin, but negative for adenovirus, CMV, EBV, HHV-8, HPV, HSV, SV 40 and p53. BRAF V600E mutation was absent. Our findings did not support the role of viruses and genetic abnormalities in the pathogenesis of LCH. In summary, the presence of a mixed population of inflammatory cells and a high content of histiocytes with characteristic cytomorphology, along with radiologic evidence and appropriate clinical findings, is highly suggestive of LCH on the intraoperative squash smears. Awareness of characteristic cytological features of LCH is necessary for rapid and accurate diagnosis. Squash smear cytology is a potentially useful tool in the intraoperative diagnosis of LCH.