Background Sanatorium Merkur was opened in 1930 by the Croatian society Merkur. The Department of Otorhinolaryngology was mentioned for the first time in 1934. During World War II, the sanatorium treated most of its insured patients, although civilians were also admitted. The research was conducted in the period from September 1, 1939 until September 2, 1945 (World War II). Aim The aim of the study was to investigate hospitalized patients in the otorhinolaryngology department in the period from 1939 to 1945. Methods Retrospective research of archival medical documentation obtained in the data on the number of patients in relation to gender and the division of the disease into four groups: trauma, inflammation, tumors and others. The data were taken from the protocol of the Surgical Clinic of the sanatorium Merkur, which are kept in the Croatian State Archives. Results The total number of patients was 1252. Inflammatory diagnoses were the most common (Furunculus accounted for 49,5%), followed by traumatic diagnoses, among which lacerocontusion wounds of the head and neck were the most common (257 patients). Tumors were found in 269 patients (21,5%) in the observed period. Most commonly there were benign tumors (atheroma of the head and neck comprised up to (51,3%). Epistaxis as the most common diagnosis in other diseases was found in 15 patients (83,3%). During the whole observed period there were no differences in the hospitalization between men and women. There were no recorded wartime gunshot or explosive wounds, but peacetime casuistry. Conclusion Since sanatorium Merkur was a private health institution, that is how patients, mostly male, were admitted and hospitalized. The admitted and treated patients did not differ in their diagnoses from other similar institutions in the city of Zagreb during the World War II, but without receiving war wounds.