The justice ministry has already placed its headquarters near St Petersburg on a list of extremist groups.
An estimated eight million people worldwide are part of the Christian-based movement, best known for going door to door looking for new converts.
It has 175,000 members in Russia and 395 branches across the country.
As the case began in Moscow on Wednesday, lawyers representing the movement submitted a counter suit, asking the High Court to declare its members victims of political repression and the justice ministry’s action unlawful.
The court ruled that this was not part of its jurisdiction, but did not say whose it was, Russia’s legal information agency reported.
The ministry argues that the Jehovah’s Witnesses’ activities “violate Russia’s law on combating extremism” and their pamphlets incited hatred against other groups.
Jehovah’s Witnesses representative Yaroslav Sivulsky told the BBC that the movement had nothing to do with extremism and he complained that in every case the courts never really listened to their arguments.