MOST of the chicken, fruit and vegetables in Ellen Devlin-Sample’s kitchen are organic. She thinks those foods taste better than their conventional counterparts. And she hopes they are healthier for her children.

Lately, though, she is not so sure.

The national outbreak of salmonella in products with peanuts has been particularly unsettling for shoppers like her who think organic food is safer.

The plants in Texas and Georgia that were sending out contaminated peanut butter and ground peanut products had something else besides rodent infestation, mold and bird droppings. They also had federal organic certification.

“Why is organic peanut butter better than Jif?” said Ms. Devlin-Sample, a nurse practitioner from Pelham, N.Y. “I have no idea. If we’re getting salmonella from peanut butter, all bets are off.”

Although the rules governing organic food require health inspections and pest-management plans, organic certification technically has nothing to do with food safety.

“Because there are some increased health benefits with organics, people extrapolate that it’s safer in terms of pathogens,” said Urvashi Rangan, a senior scientist and policy analyst with Consumers Union, the nonprofit publisher of Consumer Reports. “I wouldn’t necessarily assume it is safer.”

But many people who pay as much as 50 percent more for organic food think it ought to be. The modern organic movement in the United States was started by a handful of counterculture farmers looking to grow food using methods that they believed were better for the land and produced healthier food. It was a culture built on purity and trust that emphasized the relationship between the farmer and the customer.

By 2002, those ideals had been arduously translated into a set of federal organic regulations limiting pesticide use, restricting kinds of animal feed and forbidding dozens of other common agricultural practices.

To determine who would be allowed to use the green and white “certified organic” seal, the Department of Agriculture deputized as official certifiers dozens of organizations, companies and, in some cases, state workers.

These certifiers, then, are paid by the farmers and manufacturers they are inspecting to certify that the standards have been met. Depending on several factors, the fee can be hundreds or thousands of dollars. Manufacturers who buy six or seven organic ingredients to make one product are especially dependent on the web of agents.

If agents do a thorough job, the system can be effective. But sometimes it falls apart.

Texas officials last month fired a state worker who served as a certifier because a plant owned by the Peanut Corporation of America — the company at the center of the salmonella outbreak — was allowed to keep its organic certification although it did not have a state health certificate.

A private certifier took nearly seven months to recommend that the U.S.D.A. revoke the organic certification of the peanut company’s Georgia plant, and then did so only after the company was in the thick of a massive food recall. So far, nearly 3,000 products have been recalled, including popular organic items from companies like Clif Bar and Cascadian Farm. Nine people have died and almost 700 have become ill.

The private certifier, the Organic Crop Improvement Association, sent a notice in July to the peanut company saying it was no longer complying with organic standards, said Jeff See, the association’s executive director. He would not say why his company wanted to pull the certification.

A second notice was sent in September, but it wasn’t until Feb. 4 that the certifier finally told the agriculture department that the company should lose its ability to use the organic label.

Mr. See said the peanut company initially appeared willing to clear up the problems. But he said the company was slow to produce information and then changed the person in charge of the organic certification, further delaying the process.

He said his organization finally decided to recommend suspending the organic certification after salmonella problems at the plant were exposed.

Although certifiers have some discretion in giving organic companies time to fix compliance problems, Barbara C. Robinson, acting director of the agriculture department’s National Organic Program, said her agency is investigating the gap between the first notice of noncompliance and the recommendation that the peanut plant surrender its organic certification.

To emphasize that reporting basic health violations is part of an organic inspector’s job, Ms. Robinson last week issued a directive to the 96 organizations that perform foreign and domestic organic inspections that they are obligated to look beyond pesticide levels and crop management techniques.

Potential health violations like rats — which were reported by federal inspectors and former workers at the Texas and Georgia plants — must be reported to the proper health and safety agency, the directive said.

“For example, while we do not expect organic inspectors to be able to detect salmonella or other pathogens,” Ms. Robinson wrote, “their potential sources should be obvious from such evidence as bird, rodent and other animal feces or other pest infestations.”

Even some certifiers say that while their job is not to assure that food is safe, taking account of health inspections will help consumers.

“It’s a reassurance that they have another set of eyes, and more eyes is always a good thing,” said Jane Baker, director for sales and marketing of California Certified Organic Farmers, a nonprofit certifying organization in Santa Cruz, Calif., and one of the largest and oldest in the country. “But let’s not confuse food safety controls with the organic side of things.”

Organics has grown from an $11 billion business in the United States in 2001 to one that now generates more than $20 billion in sales, so the stakes for farmers, processors and certifiers can be high. But the agency overseeing the certifying process has long been considered underfunded and understaffed. Critics have called the system dysfunctional.

Arthur Harvey, a Maine blueberry farmer who does organic inspections, said agents have an incentive to approve companies that are paying them.

“Certifiers have a considerable financial interest in keeping their clients going,” he said.

Meanwhile, consumers are becoming more skeptical about certification, said Laurie Demeritt, president of the Hartman Group, a market research firm.

Some shoppers want food that was grown locally, harvested from animals that were treated humanely or produced by workers who were paid a fair wage. The organic label doesn’t mean any of that.

“They’re questioning the social values around organics,” Ms. Demeritt said.

The Organic Trade Association, which represents 1,700 organic companies, wants to shore up organic food’s image. This week it’s beginning a $500,000 Web-based campaign on the benefits of organic food with the slogan: “Organic. It’s worth it.”

Supporters of the National Organic Program think additional money in the recent farm bill will help improve its reach.

And great hope is being placed in Kathleen A. Merrigan, director of the agriculture, food and environment program at Tufts University, who was appointed the deputy agriculture secretary last week. Dr. Merrigan helped design the national organic standards, and is seen as a champion of organic farmers and someone who can help clarify and strengthen federal food laws.

Meanwhile, consumers remain perplexed about which food to buy and which labels assure safer and better-tasting food.

Emily Wyckoff, who lives in Buffalo, buys local food and cooks from scratch as much as possible. Although she still buys organic milk and organic peanut butter for her three children, the organic label means less to her these days — especially when it comes to processed food in packages like crackers and cookies.

“I want to care, but you have to draw the line,” she said.

But the line stops when it comes to basic food safety.

Recently, a sign near the Peter Pan and Skippy at her local grocery store declared that those brands were safe from peanut contamination. There was no similar sign near her regular organic brand.

“I bought the national brand,” she said. “Isn’t that funny?”