Clinical cytology is a diagnostic medical branch that by means of light microscopic analysis of cell and tissue specimens recognizes various physiological variations, benign and malignant diseases. Cytology is involved in diagnostics of virtually every organ and tissue. Cytology has been a separate specialization in Croatia for almost 40 years, at first as Medical cytology, later as Clinical cytology. In 2015 a new specialization was introduced, synthesizing cytology and pathology, and is called “specialization in pathology and cytology”. From the very beginning, cytology is closely connected to clinics, and the best results are achieved in team work of the cytologists and clinicians of different specialities, and in direct contact with the patient. As minimally invasive and rapid diagnostic method, with almost no contraindications and rare and minor potential complications, cytology is extremely attractive diagnostic method, especially considering that cytological specimens are convenient for ancillary diagnostic methods such as flow cytometric immunofenotypization, cytogenetic, molecular techniques. In this paper we discuss the role of cytology in the diagnostics of some organ systems, as well as its advantages and limitations, and factors that influence the end the result and quality of cytological findings. Particular attention should be paid to the quality of sampling, and specimen preparation techniques. It is of utmost importance that all phases of the procedure are performed by adequately educated medical staff. Cytological analysis is an indispensable diagnostic procedure for early detection, diagnosis and follow-up of various, especially inflammatory, benign, premalignant and malignant conditions in various organs and organ systems.