Upon their return, the Soviets undertook even stricter repressive measures than those before the war. In the course of 10 years, approximately 130,000 of the population were deported to Siberia and other distant areas of the Soviet Union: the majority of them perished due to the unbearable transport and living conditions.

A partisan war ensued, lasting 9 years and claiming tens of thousands of lives.

It has been calculated that Lithuania lost approximately 30% of its population during the period 1940-53.

As early as the first post-war years, a mass immigration of Russians and other Soviet nationalities was begun, bringing unavoidable sovietisation and russification of public life. Once again, as in the 19th century, the Lithuanian language faced the danger of extinction.

The Soviet decades brought about a basic change within the country's economy and infrastructure: land was nationalised and turned over to the collective farms, rural life was threatened and a new movement of the population towards the cities, with unrestrained industrialisation of the country, ensued. All this took place without reference to Lithuania's internal needs and opportunities. The country's economy was developed solely through the methods of the occupying regime. Construction was implemented of giant complexes manufacturing fuel-injecting equipment, machine tools, chemicals, oil, mineral fertilisers and processing metal, none of which reflected Lithuania's needs. This entire infrastructure functioned on the basis of imported raw materials and energy resources. It employed tens of thousands of workers who immigrated into Lithuania.

During the 1980's, one of the largest nuclear power stations in Europe was constructed near Ignalina in northeastern Lithuania.