The Skopje district court found the defendants guilty of weapons possession and belonging to a terrorist group, presiding judge Lidija Nedelkovska said, announcing the ruling.
The court jailed one man for 12 years, and imposed 10-year terms on another 12. Four alleged group masterminds were convicted in absentia and each sentenced to 15 years in prison. Macedonian authorities have issued international warrants for their arrest.
The weapons were seized in November 2007, during an operation to capture Lirim Jakupi, an ethnic Albanian former rebel who escaped from prison in Kosovo.
Jakupi escaped but police arrested the 13 defendants in and around the mountain village of Brodec, where they discovered laser-guided anti-aircraft missiles, artillery pieces, rocket-propelled grenade launchers, sniper rifles, assault rifles, and other weapons.
Six suspected extremists were killed in gun battles with special police officers.
Brodec, in the volatile area at Mountain Sara, was the center of an 2001 uprising by ethnic Albanian rebels.
Ethnic Albanians make up about a quarter of Macedonia's 2 million people.