Fine-needle aspiration biopsy (FNAB) is currently the first line investigation for the diagnosis and triage of head and neck masses. Cytomorphological evaluation of FNAB specimens allows a diagnosis in many cases. However, there are many challenging diagnostic areas in the head and neck including thyroid neoplasia, salivary gland neoplasia, and lymph nodes. Important advances in FNAB diagnosis have been made over the last decades, especially with the routine use of several ancillary techniques and markers on FNAB specimens that have allowed optimizing the cytomorphological diagnosis, and have reshaped the practice of cytopathology. In this thesis, we discuss the major role and limitations of FNAB for the diagnosis of thyroid nodules, cervical lymphadenopathies and salivary gland lesions. We cover some of the current challenges in these areas, selected diagnostic pitfalls, and recent advances including ancillary techniques such as immunocytochemistry and molecular analyses that can be applied on FNAB samples.