Delays might not be the only thing disrupting your subway commute.

Paranormal experts say apparitions are roaming the more than century-old transit system -- including spirits at the City Hall stop, a phantom train at Astor Place, and the beloved dog of former President Franklin D. Roosevelt.

There have been at least three documented hauntings of stations, according to Phil Schoenberg, who runs "Ghost Walks of New York." He offers walking tours of haunted areas in the city and has a doctorate in history from New York University.

One involves Fala, the trusted Scottish terrier companion of FDR. The president often traveled with her from Grand Central to the Waldorf-Astoria Hotel through a secret entrance and elevator. "He took the dog wherever he traveled," Schoenberg said.

Sometimes, subway riders can spot the dog on the Grand Central platform -- lingering where he once waited with his owner. He also sometimes haunts Washington Square Park, according to Schoenberg.

Straphangers have also spotted a phantom train at Astor Place -- and at least one rider has reported boarding it, Schoenberg says.

The apparent spectral train belongs to August Belmont, Jr., whose company built the Lexington Avenue line that opened in October 1904. Belmont maintained his own private car, which he used to entertain guests -- and it would carry him to the racetrack that was named after him in Queens, according to Schoenberg. The car was lavishly decorated, with leatherette curtains, a reclining couch, mahogany and silk drapes, even a stove. Drinks were served on board.

How to explain its spottings at the Astor Place stop? "What appears to be a haunting might really be a sudden shift in time, an occurrence that's been termed retrocognition," wrote Tom Ogden in his book "Haunted Greenwich Village: Bohemian Banshees, Spooky Sites, and Gonzo Ghost Walks." "Such displacements are extraordinarily rare, instantaneous, and usually very brief."

Paranormal authorities also say that the original City Hall subway station, closed now, is haunted. When workers were building it in the beginning of the 20th century, they heard strange noises.

"They realized they were words being chanted," Schoenberg said, by the spirits of Lenape Indians who died in a nearby massacre hundreds of years ago.

Subway riders also told amNewYork they have had their own experiences with ghosts.

Fred Malave, 37, a sales associate at Mr. Throwback in the East Village, said his 6-year-old Nasir performs in the subway -- and often sees his father, who passed away.

"My son says he see things, spiritual stuff like my Dad, he describes my dad to a T," he said.

He believes his late grandfather watches over his son while he breakdances in stations -- and keeps him safe.

"The subway is super haunted, it just is inherently," said Claudia Nagy, 21, of the East Village. "It's ancient, it's really old, but also karmically, a lot of destruction went into building them and I think it's an easy pathway for things to move around in."

Nagy recounted a strange experience one night on the No. 1 train alone. The subway door wouldn't close, and kept opening repeatedly.

"They kept almost closing up, but they kept opening up again and again. It was me alone in a car and the doors kept acting like someone was in them, they wouldn't open or close all the way," she remembered.

The MTA sounded a skeptical note about it all.

"While it's tempting to blame ghosts for the occasional signal problem or equipment delay, we'll keep our focus on the more than 6 million real live customers who ride the subway on our busiest days," spokesman Adam Lisberg said.