"The thing that made him such a great runner may have killed him," Ryan's father Joe Shay said.
Ryan and other top athletes underwent medical testing in Flagstaff, Arizona, where he trained, last spring, Joe Shay said, and he was cleared for running.
"He said the doctors told him that because your heart rate is so low, when you're older you may need a pacemaker to make adjustments on that," said Joe Shay, adding his son first was diagnosed with a larger than normal heart at age 14.
Scientists long have noticed the phenomenon of the "athlete's heart." Athletes who train hard in aerobic sports, such as cycling, running or swimming, tend to have a bigger heart that pumps more blood throughout the body.
The 28-year-old Ryan Shay collapsed about 5 1/2 miles into the race that would stretch another 21 miles.
"I got a call that Ryan had fallen down ... then I got another call that his heart had stopped," Joe Shay said.
The medical examiner's office said an autopsy will be performed Sunday.
"It's a big loss for the running community," said 2004 Olympic women's marathon bronze medalist Deena Kastor, who used to train with Shay in California. "It's a day we should be celebrating. It has cast a pall."
A statement from USA Track & Field said Shay immediately received Cardiopulmonary resuscitation (CPR). He was taken to Lenox Hill Hospital, where he was pronounced dead on arrival at 8:46 a.m., according to New York City police.
A recreational runner died during last month's Chicago Marathon, the warmest in that event's history. But the death of an elite athlete during a major competition is a rare and startling occurrence.
At the 2004 Olympic men's marathon trials, Shay was a favorite going in but was hampered by a hamstring strain and finished 23rd.
Shay was born May 4, 1979, in Ann Arbor, Michigan, the fifth of eight children in a running family. His parents are the cross country and track coaches at Michigan's Central Lake High School.
"He achieved through hard work and effort goals and dreams that most people will never realize," Joe Shay said. "He was a champion, a winner and a good person. ... He used to say, 'Dad, there's a lot of guys out there with a lot more talent than me, but they will never outwork me."'
Shay was a five-time national road racing champion, winning the 2003 U.S. marathon, 2003 and 2004 half-marathon, 2004 20k and 2005 15k.
"He was a tremendous champion who was here today to pursue his dreams," said Craig Masback, CEO of USA Track & Field. "The Olympic trials is traditionally a day of celebration, but we are heartbroken."