Achatz, 34, beat four other chefs with wide-ranging culinary styles – Suzanne Goin, Frank Stitt, Jose Andres and Dan Barber – to win this year's James Beard Foundation's outstanding chef prize.
"I look at the award as the point of starting over," Achatz said after a glitzy prize-giving ceremony at New York's Lincoln Center hosted by actress Kim Cattrall from "Sex and the City" and celebrity chef Bobby Flay.
Achatz, a leader in molecular gastronomy or progressive cuisine, runs one of the most respected restaurants in the United States. Alinea, which opened in Chicago three years ago, has been a showcase of his inventive techniques and artful presentations.
The award comes after a tough year. Just 12 months ago, Achatz's tongue had swollen so badly that he was not speaking clearly and had lost much of his taste.
But Achatz, instead of accepting a fate that would have ended his career, chose a less drastic if unproven combination treatment that included radiation and chemotherapy. He announced last December that he was free of cancer.
Writing a cookbook from the hospital bed
During his treatment, he barely stopped working at Alinea and was writing a cookbook on his laptop in the hospital which will be published in September. He is also planning to open a second restaurant in Chicago.
Achatz said the "tenacity and drive" he learned during his apprenticeship at The French Laundry restaurant in Yountville, California, taught him not just how to cook but also how to survive.
While Alinea stakes claim as the new kid pushing culinary boundaries from the US Midwest, two standard bearers in New York City were recognised in other top James Beard prizes this year.
The outstanding restaurant award went to Gramercy Tavern, which was opened in 1994 and is known for its new American culinary, while celebrity chef Mario Batali and wine expert Joe Bastianich were selected as top restaurateurs for their lauded 10-year-old Italian eatery, Babbo Ristorante e Enoteca.