Jorge Alberto Mendez, 42, was arrested Saturday while trying to cross into Mexico from El Paso, Texas, where he lives, said regional Deputy Attorney General Alejandro Pariente.
Pariente said the investigation began in April 2008 with the rape of a 15-year-old girl. Similar cases were subsequently reported.
One of the victims managed to write down the license plate number of her assailant, which eventually led to Mendez's arrest, Pariente said.
Ciudad Juarez, a battleground in Mexico's drug war, has a history of violence against women.
During the decade that ended in 2003, more than 100 women disappeared in the city. Many of them were young women last seen in the city's downtown area or after boarding buses. The victims' bodies were often dumped in the desert outside the city.
Last year, a Mexican citizen who allegedly confessed to killing at least 10 women in Ciudad Juarez was extradited from the United States to stand trial for aggravated homicide.
In 2007, a New Mexico man was accused of repeatedly crossing into Ciudad Juarez and raping at least 13 women in their homes.
Pariente said Mendez prowled residential neighborhoods during the day and attacked at night, sometimes entering bedrooms through windows. He allegedly threatened his victims
-- between 13 and 20 years old -- with a gun.
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