The story, written by investigative reporter Nancy Phillips, documents Conlin's alleged molestation of more than one underage girl decades ago.
Conlin has hired an attorney to defend himself, according to Deadspin, which first reported that Conlin had resigned due to the accusations.
"Mr. Conlin is obviously floored by the allegations, which supposedly happened 40 years ago," George Bochetto, Conlin's attorney, is quoted as saying by the Inquirer and CBS Philly. "He has engaged me to do everything possible to bring the true facts forward and to vindicate his name."
Conlin is known for his abrasive commentary, which made him the perfect mouthpiece for Philadelphia's fans. He is therefore widely read but not beloved like some other long-tenured columnists.
He wrote a column in November about the public reaction to the allegations against former Penn State football coach Jerry Sandusky, who is accused of sexually abusing an ever-growing number of young boys. Conlin took to task people who claim they would "pound the snot" out of the former coach.
"Everybody says he will do the right thing, get involved, put his own ass on the line before or after the fact," Conlin wrote. "But the moment itself has a cruel way of suspending our fearless intentions."
Conlin was named to the writer's wing of the Baseball Hall of Fame this summer.
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