BALTIMORE — The time-honored, widespread and mostly hidden practice of sign-stealing in baseball was thrown into scandal Tuesday with a report saying Major League Baseball had confirmed the New York Yankees’ accusations that the rival Boston Red Sox had stolen their catchers’ signs and relayed them to their own hitters with the help of an Apple Watch.

According to the New York Times report, the Yankees filed a detailed complaint with the commissioner’s office two weeks ago that included video the Yankees had shot of the Red Sox dugout during a series at Fenway Park on Aug. 18-20. In the video, the report said, a member of Boston’s training staff could be seen looking at his Apple Watch in the dugout and then relaying information about pitch type and location to Boston players.

At Oriole Park at Camden Yards, where the Yankees were set to play the Baltimore Orioles on Tuesday night, Yankees Manager Joe Girardi confirmed the outline of the Times report about the Red Sox, saying, “It’s something we’ve suspected,” but he declined to discuss specifics about the complaint or the investigation.

According to the Times report, the Red Sox also filed a countercomplaint accusing the Yankees of similar electronic sign-stealing measures, using cameras from the Yankees’ YES Network. Asked about those accusations, Girardi said, “No chance.”

In Boston, where Commissioner Rob Manfred was making a regularly scheduled appearance at Fenway Park, he largely downplayed the story, confirming only that the accusations were made and saying that an investigation is ongoing and will be resolved soon.

“To the extent that there was a violation on either side,” Manfred said, “ … we are 100 percent comfortable that it is not an ongoing issue.”

The accusations come as the Red Sox are attempting to hold off the fast-closing Yankees in a battle for the American League East title. After winning three of four from Boston last week at Yankee Stadium, then winning Monday at Baltimore, the Yankees, who also lead the AL wild-card race, moved to within 2 1/2 games of the Red Sox entering Tuesday night’s games. The teams do not play each other again this season.

“When you have the kind of rivalry that the Yankees and Red Sox have,” Manfred said in Boston, “I guess it’s not shocking you could have charges and countercharges like this.”

According to the Times report, which cited “several” unnamed people familiar with the matter, the Red Sox, after being presented with the evidence, admitted to MLB that their trainers had received signals from video-replay personnel and then relayed that information to players, in a practice that had been ongoing for at least several weeks. The Red Sox told MLB, however, that Manager John Farrell and president of baseball operations Dave Dombrowski were not aware of the practice.

While sign-stealing — mostly by base runners on second base, who have a mostly unfettered view of the catcher — has been an accepted part of baseball gamesmanship for decades, it has caused occasional rifts when the practice becomes too obvious. And in the case of Boston’s accused transgressions, it was the illicit use of electronic devices that could land the organization in trouble.

“We actually do not have a rule against sign-stealing, and it has been a part of the game for a very, very long time,” Manfred said in Boston. “ … It’s the electronic equipment that creates the violation. And I think the rules against electronic equipment has a number of policy reasons behind them, but one of them is we don’t want to escalate attempts to figure out what a pitcher’s going to throw by introducing technology or electronics into that mix.”

At a news conference in Boston, Dombrowski downplayed the accusations, at one point laughing when asked if he thought sign-stealing, in and of itself, was wrong.

“No, I don’t,” Dombrowski said. “I guess it depends on how you do it. But, no, I never thought it was wrong. I’d guess everybody in the game has been involved with it throughout the years. People are trying to win however they can. It’s an edge that they try to gain. Sometimes the sophistication of [catchers’] signs can make a difference.”

Dombrowski also implied the Yankees had chosen to leak the story on Tuesday because they knew Manfred would be at Fenway Park and thus accessible to reporters.

It was unclear what penalties Manfred was considering should he find either team guilty of breaking the game’s rules, but he all but ruled out the possibility of vacating wins, saying there is no precedent for any such punishment. The most likely penalties would be a fine and/or the loss of one or more future draft picks.

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