In the early 20th century, many armies suffered from venereal diseases. Lithuanian army that participated in the Wars of Independence (1918–1920 [1923]) was no exception. Although venereal diseases did not claim many lives, they forced small army to give up the services of many soldiers. Historical analysis of archival documents of the Lithuanian Ministry of National Defense, military periodicals, Statutes and medical books of the Lithuanian army from the period 1918–1923, has been conducted. The venereal disease that bothered the Lithuanian army the most was gonorrhea accounting for 78.4% of the overall incidence of venereal diseases in 1919. The Sanitation Department of the Lithuanian Ministry of National Defense took strict measures to stop the spread of gonorrhea and other venereal diseases. This institution paid attention to regular health examinations, registration of patients, disease traceability, education, preventive treatment, isolation, and prostitution. In case of illness, treatment was carried out in a special hospital named II Separate Infirmary. Until 1923, the treatment was compulsory even to soldiers who have completed their service. Difficulties were encountered in different areas because the soldiers avoided treatment, hid their illness, and visited uneducated doctors. There was a lack of laboratories to carry out the research, and the treatment of the patients was expensive and harmful. Despite all the difficulties, the fight against venereal diseases in the Lithuanian army was won. In 1923, the incidence of gonorrhea was twice as low. The incidence of other diseases has also decreased. Having carried out its main work the Sanitation Department narrowed its activities in 1923.