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Lithuanian national meteorological service was established in 1921. The present Lithuanian Hydrometeorological Service formed gradually by taking over the functions of the Military Meteorological Service from the Ministry of National Defence, the functions of the Hydrological Service from the Ministry of Transport and Communications, and the functions of the Climatological Institute from the Ministry of Education. Meteorological observations in Lithuania originated at Vilnius University in 1770.

First river observations were made on Nemunas by Smalininkai in 1803, and first marine observations – on Curonian Lagoon in 1880. Interwar Lithuania progressed to aerosonde and phenological observations, though irregular. In 1945, Lithuania launched its first radiosonde and started agrometeorological observations.

Further development included origination of solar radiation (1952), water quality on Baltic Sea and Curonian Lagoon (1959), river and lake pollution (1964), radar (1974), total ozone (1993) and ultraviolet solar radiation (2002) measurements.

In 1992, Republic of Lithuania has joined the World Meteorological Organisation (WMO) – a specialized United Nations agency – and ever since the Lithuanian Hydrometeorological Service represents its country in WMO, though international relations of Lithuanian national meteorological service can be traced back to 1929. In 2005, Lithuania became a cooperating state with the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT). Similar cooperation agreement with the European Centre for Medium-Range Weather Forecasts (ECMWF) entered into force in November 2006.