The 54-year-old was found at his Lincoln Park home Tuesday morning and was taken in critical condition to Northwestern Memorial Hospital, where he was pronounced dead, fire officials said.
There were no signs of foul play, according to police.
Celebrity chef Atul Kochhar tweeted Tuesday that they lost a hero.
Longtime Chicago magazine food writer Jeff Ruby tweeted "I can't believe I am typing these words," before sharing the news.
"Today we mourn the loss of a Chicago culinary legend," Fireside restaurant in Ravenswood tweeted.
Matthias Merges, in an interview with DNAinfo Chicago, said his boss of 14 years was a game changer.
"It's a shock," said Merges, who was his second-in-command. "We could never devalue the enormity of what he accomplished and the changes he made to the face of American cuisine, and I think even though he had his own issues, the greatness of what the restaurant was trumps it all."
Merges left Trotter's and the fine-dining world to open Yusho, serving Japanese street-food; the cocktail bar Billy Sunday, and his newest restaurant, A10. Trotter's influence is in all three, Merges said.
"What was most innovative was this new way of thinking about food and service and restaurants in general," Merges said. "It's like an undying fire, to really create an experience for clients that transcends mediocrity. It's something we've always tried for."
Homaro Cantu of moto and iNG said of Trotter's influence: "I wouldn't be here. I wouldn't be married to my wife if it hadn't been for Charlie Trotter," said Cantu, who was a cook when his now-wife did a one-day guest-chef stint at the restaurant, a gift from a friend.
Both Cantu and Merges recalled Trotter's incredible drive and pursuit of perfection that put him ahead of his time.
In 1987, Trotter opened Charlie Trotter's, a restaurant that became known as one of the world's best, earning a two-star Michelin rating before he closed it in August 2012.
Trotter won a number of awards from the James Beard Foundation, including best chef in the Midwest in 1992, the nation's outstanding chef award in 1999, the nation's outstanding restaurant in 2000. In 2000, he also was awarded Best National Television Cooking Show for "The Kitchen Sessions, with Charlie Trotter."
Read more reactions to Trotter's death here:
Rest In Peace Charlie Trotter. A giant. A legend. Treated shabbily by a world he helped create. My thoughts go out to those who loved him.— Anthony Bourdain (@Bourdain) November 5, 2013
Trotter had famous temperament, stern stubbornness but if you knew him he was all about vision and leadership and technique. #sadday— Andrew Zimmern (@andrewzimmern) November 5, 2013
Its a big loss for Chefs world to loose a hero like Chef Trotter - we will miss him. http://t.co/xmVzumQvEM— Atul Kochhar (@atulkochhar) November 5, 2013
So sad to learn of Charlie Trotter's passing. The world has lost a culinary icon.— SAVEUR (@SAVEURMAG) November 5, 2013
We are deeply saddened by the passing of Charlie Trotter. He will always be remembered for his talent and vision.— Beard Foundation (@beardfoundation) November 5, 2013
CHARLIE TROTTER: chef, mentor, trailblazer, philosopher, artist, teacher, leader. He now belongs to the ages.— GRAHAM ELLIOT (@grahamelliot) November 5, 2013
Collectively, this entire industry will be wishing Charlie Trotter a peaceful journey on when they hear the news. RIP, Chef. And thank you.— Trenchermen (@Trenchermen) November 5, 2013
When my car was stolen in 1995, the only thing I cared about was that the Charlie Trotter cookbook was on the back seat :(— Lesley Chesterman (@lesleychestrman) November 5, 2013
Charlie’s Trotter will always have a seat at the table among Chicago’s legendary figures. http://t.co/wTyoxLijcf— ChicagoMayorsOffice (@ChicagosMayor) November 5, 2013
Sad to hear if the death of Charlie Trotter. My first fine dining meal over 20 years ago. I still remember everything I ate!— Bake (@BakeChicago) November 5, 2013
God bless Chef Charlie Trotter's family.Chicago and America lost a bright lightXOArt and Jesus— Chef Art Smith (@ChefArtSmith) November 5, 2013
Every meal at #charlietrotter was a magical mystery tour: Buddha's hand. Araujo syrah, matsutake mushrooms three ways, the kitchen tour.— Bess Gallanis (@BessGallanis) November 5, 2013
trotter. You made a huge difference to me and lea that night in 2001.felt like I learned everything in one moment.Everything I didn't know.— lula cafe (@lulacafe) November 5, 2013
I've never been more excited about the prospect of dining than I was the night I knew I was visiting Trotters. Never before. Never since.— Michael Nagrant (@MichaelNagrant) November 5, 2013