Fine needle aspiration is a minimally invasive, low-morbidity, and cost-efficient technique for the sampling of mediastinal lesions. Additionally, ancillary testing on FNA samples can be used for the refinement of diagnoses and for treatment-related purposes (flow cytometry, cytogenetics, immunohistochemistry, and molecular diagnostics). Mediastinal lesions, however, can show a variety of lineages and morphologic features, giving rise to diagnostic dilemmas. As a result, the differential diagnosis can vary widely and becomes especially challenging due to the smaller sample size on FNA and the variability in component sampling. For appropriate patient management and to determine the correct treatment strategies, accurate pathologic diagnoses are paramount. In this review, we present the cytomorphologic features together with the immunophenotypic findings of mediastinal lesions, with emphasis on the diagnostic challenges and pitfalls in FNA cytology samples, including smears and cell block sections.