It used data collected from a Centers for Disease Control and Prevention survey called the Behavioral Risk Factor Surveillance System.
The top 177 metro areas in the nation were evaluated, and St. Joseph came in at 176, behind cities like Detroit, Michigan and Jersey City, New Jersey and ahead of only New York City.
According to the St. Joseph Health Department, the Harvard study used CDC data that shows people in St. Joseph exercise less, eat and smoke more and are generally less healthy.
"If you enjoy good health, you just feel better," said Stephanie Malita from the St. Joseph Health Department. "People that aren't healthy worry about bills from the hospital. They worry about things like how do I get to the grocery store."
The city is tackling the health issue with programs like Live Well St. Joe, promoting opportunities to help people make healthier choices like kids growing their own vegetables in schools.
"Part two is that we've done cooking classes for people that don't know what to do with fresh zuchini or tomatoes or whatever they've collected from the garden," Malita said. "We've taught them how to use it."
So what cities are at the top of the list? Surprising to some, all top five cities ranked as the most happy are in Louisiana.
"When we're looking at data like that, it doesn't strike me as a state that would rank high on a happiness scale," Malita said. "If you look at education levels and poverty levels and health initiatives, I wouldn't think they'd be better off than Missouri."
There was definitely dissent locally with the survey results.
"I resent those remarks," said St. Joseph City Council member Joyce Starr. "I think he needs to come here and visit before he writes that kind of stuff. Come visit, talk to us, meet us because we are good people and we are happy people."
"I'm not buying in," Malita said, also disagreeing with the survey results. "I don't care if it comes from Harvard or not."