The Yale School of Medicine’s decision to accept a fellowship grant from PepsiCo could lead to biased research, some food activists are saying.

These activists have criticized the soft-drink giant’s decision in December to sponsor a graduate fellowship in the school’s M.D.-Ph.D. program, worth $250,000 over five years, for students who want to perform research on nutrition and obesity-related diseases. The relationship between the School of Medicine and PepsiCo, these activists say, will lead to findings that overstate the health of Pepsi products — a charge that School of Medicine Dean Robert Alpern refuted.

Michele Simon SPH ’90, a public health lawyer who has written a book that argues that the food industry undermines the health of Americans, said PepsiCo is being disingenuous in its desire to research nutrition to improve its products.

“They make some healthier things, but the profit drivers of their portfolio include Pepsi, Gatorade and a whole litany of unhealthy beverages,” she said. “They own Cheetos, for God’s sake.”

New York-based chef and blogger Rob Endelman said the fellowship and laboratory will produce biased results that will benefit PepsiCo’s bottom line. The financial relationship between the company and the University sends the wrong message about scholarly research, he added.

“If [PepsiCo] were really trying to do better, they would not be in the business of selling Pepsi,” he said. “Everything big food companies try to do is predicated on making money and trying to sell their products.”

Alpern, who has received a series of e-mails from the activists, said the school had done nothing wrong in accepting PepsiCo’s grant.

“We don’t see PepsiCo as an evil company,” Alpern said. “We feel [the gift] is perfectly ethical.”

Because the grant to the M.D.-Ph.D. program was unrestricted, meaning the school can use the funding as it chooses, the School of Medicine was justified in accepting the money, Alpern said.

“A good analogy is the opinion that tobacco companies giving schools grants may promote cigarette smoking,” Alpern said. “A lot of schools won’t take tobacco money, [but] we don’t have a ban against taking money from anyone in the food industry.”

PepsiCo spokeswoman Michelle Naughton said she was surprised to hear of their activists’ concerns; the sole focus of the corporation’s research initiative, she said, is to develop healthier products. PepsiCo, she added, has recently committed to reduce sugar, sodium and saturated fats in its products while increasing whole grains, fruits and vegetables.

James Jamieson, the director of the School of Medicine’s M.D.-Ph.D. program, said the researchers working in the PepsiCo laboratory are respected physicians who are genuinely concerned about nutrition. He added that the research supported by the fellowship is important for the field of nutritional studies.

“PepsiCo is doing a philanthropic thing,” Jamieson said. “People [are going] overboard by not recognizing that PepsiCo is trying to rectify its [image].”

PepsiCo opened its ninth global research laboratory at 25 Science Park in early January as part of an initiative to improve the nutritional value of its products. Students who receive the graduate fellowship may choose to work at the PepsiCo laboratory.

On March 16, PepsiCo announced a voluntary policy to stop selling full-sugar soft drinks to primary and secondary schools worldwide by 2012.