ROCHESTER — The Lake Shore Limited runs between Chicago and New York City without crossing the Canadian border. But when it stops at Amtrak stations in western New York State, armed Border Patrol agents routinely board the train, question passengers about their citizenship and take away noncitizens who cannot produce satisfactory immigration papers.

“Are you a U.S. citizen?” agents asked one recent morning, moving through a Rochester-bound train full of dozing passengers at a station outside Buffalo. “What country were you born in?”

When the answer came back, “the U.S.,” they moved on. But Ruth Fernandez, 60, a naturalized citizen born in Ecuador, was asked for identification. And though she was only traveling home to New York City from her sister’s in Ohio, she had made sure to carry her American passport. On earlier trips, she said, agents had photographed her, and taken away a nervous Hispanic man.

He was one of hundreds of passengers taken to detention each year from domestic trains and buses along the nation’s northern border. The little-publicized transportation checks are the result of the Border Patrol’s growth since 9/11, fueled by Congressional antiterrorism spending and an expanding definition of border jurisdiction. In the Rochester area, where the border is miles away in the middle of Lake Ontario, the patrol arrested 2,788 passengers from October 2005 through last September.