The green woodland of Aukštieji Paneriai was a favourite summer resort of Vilnius holidaymakers. In 1932, a settlement was planned here according to the Garden City concept created by architect Ebenezer Howard, which was very popular at the time and was supposed to balance urban and rural advantages. The settlement was named Jogailaičiai (Jagiellonowo) after the Jagiellonian dynasty of kings of Poland and Lithuania. The expansion of Jogailaičiai was focused on the development of health and sports areas. In 1939, Paneriai was granted the status of a resort.
The development of Paneriai was interrupted by World War II. On 1 September 1939, Nazi Germany invaded the Republic of Poland. According to the secret Ribbentrop-Molotov pact, on 17 September, Poland was also invaded by the Soviet Union which occupied Vilnius two days later, on 19 September. Following the Soviet–Lithuanian Mutual Assistance Treaty signed on 10 October 1939, Vilnius was returned to Lithuania, and Lithuania allowed the Soviet military troops to be established across the country. It did not take long for the Soviet Union to occupy Lithuania on 15 June 1940. To the east of Jogailaičiai, a Soviet military airfield was established, and the construction of a service fuel base was started.
Within a few months, working in two shifts, seven pits for fuel tanks (5-7 m deep and 20-35 m in diameter) were excavated, including trenches connecting these pits, where the fuel pipeline was to be installed. Workers and locals called the place ‘the base’. They only managed to pave the walls of two or three pits with outdoor stones. Two narrow-gauge railway lines were built into the territory. The site of 5 ha, as a military object, was surrounded by a fence with barbwire at the top. The total area of the fuel base covered 30 ha. However, it was not finished due to the invasion of Nazi Germany on 22 June 1941.
In 1941–1944 Paneriai became one of the largest sites of mass killings of Jews in Europe. From 1941 to July 1944, up to 70,000 people were executed in Paneriai. The vast majority of victims were Jews from Vilnius and Eastern Lithuania. In 1942–1943, around 2,000 fighters of Polish underground resistance organisations, several thousand Soviet prisoners of war, as well as Roma, Lithuanian soldiers and other residents who did not comply with the occupation regime were shot to death here for political reasons.