Pittsburgh and Syracuse made plans to leave for the Atlantic Coast Conference in September, and West Virginia bolted for the Big 12 the following month. The Big East regrouped by adding Central Florida, Houston, Memphis, SMU and Temple for all sports and Boise State, San Diego State and Navy for football only.
Marinatto told The Associated Press on Monday that trying to guide the conference through realignment took a physical and mental toll on him.
He said he began talking to the conference presidents in mid-April about stepping down.
"I've been running a marathon not only for the last eight months but for the last 2½ years," he said. "As fulfilling as it can be, it is equally draining. All the assets are in place right now (in the Big East). It's probably time for a commercialized kind of perspective. Clearly the collegiate model is dead."
Marinatto became the third commissioner of the Big East on July 1, 2009. He had served as the conference's senior associate commissioner since 2002 and spent 14 years as the athletic director at Providence College.
"John helped build the Big East into what it is today, and played a critical role in our successful expansion efforts, and for all of that we thank him," said Judy Genshaft, President of the University of South Florida and the chair of the conference.
But privately, many in the conference were unhappy by the defections of Pitt and Syracuse, and some blamed Marinatto for being caught off guard, having just turned down a television contract offer from ESPN last spring.
Former Commissioner Mike Tranghese, who retired in 2008, said his successor "inherited a very, very difficult situation."
"I said that when I left that's one of the reasons why I did leave," he told The Associated Press on Monday. "The conference was susceptible to being raided."
"When something goes wrong, the person in that chair is the one to take the hit."
Connecticut President Susan Herbst was asked if the league's presidents had sought Marinatto's resignation.
"It was entirely John's decision," she said in an email to The Associated Press. "Let me add: He did a stellar job this past year, enabling the Big East to move forward. We are strong now, thanks to his efforts and tireless work in a very fluid environment."
The news caught some Big East schools off guard.
"You're never surprised in our business about things, but I would be less than honest to say I saw this coming," said Bill Bradshaw, Temple's athletic director. "Yes, in our business you're never surprised. But John's a first-class individual, straightforward. A good man. High integrity. A nice person. Whenever someone resigns, it's something you reflect."
Connecticut Athletic Director Warde Manuel said the move will not affect his school's affiliation with the Big East.
"Our relationship is with the conference, and we'll look forward to working with the leadership in the conference to move forward," Manuel said.
Connecticut provided Marinatto with some of the conference's biggest moments during his tenure, winning national championships in men's basketball in 2011 and in women's basketball in 2009 and 2010.
But UConn had been actively exploring the possibility of joining the Atlantic Coast Conference or another conference after the moves by Syracuse and Pittsburgh.
Manuel said Monday that UConn has no current plans to leave.
"I'm happy in the Big East," he said. "That's where we're going to stay and compete and do what we do."
Other schools, including Providence, Marquette, and even Syracuse issued statements wishing Marinatto well.
"We know he tried his best and worked relentlessly," Syracuse Athletic Director Daryl Gross said. "We wish him the best."
Former Miami Dolphins CEO Joseph Bailey III will serve as interim commissioner. The search for a permanent replacement will be chaired Gregory Williams, the president of the University of Cincinnati and a member of the Big East executive committee.
The conference also announced that as part of an effort to maximize its media rights and branding, it had retained The Boston Consulting Group to review its organizational design and structure.
The league is facing a critical juncture, with negotiations on a new television contract set to begin in the fall. Questions remain about whether the new-look Big East can draw the type of billion dollar media rights deals that other power conferences have locked up over the last year.
Most of the new members won't be in place until 2013.
And how much revenue the Big East will receive from a restructured BCS is also to be determined.
"At some point, we want to have a stable environment over conference affiliation and alignment," Manuel said. "The bottom line, is that we need to get to a place where everything is stable."
Marinatto said he had no idea when he was negotiating TV rights a year ago, that the conference landscape would change so much in just a few months. But, he said he made the best decisions he could as commissioner, given the changing environment.
"A lot of things I think I would have done differently, but you do the best you can with the information you have at the time," he said.
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