The 86-year-old former general is the first former Latin American leader ever found guilty of such a charge.
A three-judge tribunal issued the verdict after the nearly two-month trial in which dozens of victims testified about horrific atrocities.
Prosecutors said Rios Montt must have had knowledge of the massacres of Mayan Indians when he ruled Guatemala from March 1982 to August 1983 at the height of the country's 36-year civil war.
Rios Montt said he never knew of or ordered the massacres while in power.
The war between the government and leftist rebels cost more than 200,000 lives and ended in peace accords in 1996.