Earlier this week, a lower court outlawed the parade after the chief prosecutor argued that anti-gay groups could cause violence.
As in many other former Soviet republics, gay rights is a sensitive issue in Lithuania, which has repeatedly been criticized by human rights groups for widespread intolerance toward sexual minorities.
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No major gay pride events have been held in the largely Catholic country of 3.4 million since it regained independence in 1991.
The Supreme Administration Court rejected the lower court’s decision, and ruled that the state must ensure the right to peaceful assembly.
The Baltic Pride event in the Lithuanian capital, Vilnius, is expected to draw 350 participants and an even larger crowd of opponents.