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MANHATTAN (PIX11) — From meat and produce, to cheese, eggs and milk, do how you know how clean your grocery store is?

An undercover investigation by PIX11 News revealed the city’s filthiest grocers, exploring all five boroughs and the markets that failed their state health inspections over the course of a year.

The state worked for months to give us those 5,000 pages of reports, which led us to your grocery aisles equipped with an undercover camera.

We found disgusting, unsafe and filthy conditions that easily could make your family sick.

Whole Foods boasts a wholesome reputation, based on its plethora of organic offerings. But what state inspectors found was anything but tasty.

In the most recent reports available to us, their New York City stores failed eight inspections in a one-year period.

PIX11’s cameras found mouse droppings in the bakery and beer sections at the Whole Foods in Columbus Circle.

They were also cited for keeping foods on the breakfast buffet and custom toppings at the pizza station at the wrong temperatures. Inspectors counted up live flies and found dried food residues and grime near the meat work area.

They were fined $1,200 for the violations.

Food sanitation expert Peter DeLucia, the assistant commissioner of Westchester County’s Department of Health, says too often grocers have their priorities wrong.

“The establishment isn’t doing its job and what happens a lot of the time is their number one priority is selling food,” DeLucia said. “It’s not public health or public health protection.”

No manager was available at the Columbus Circle grocery store and Whole Foods declined to provide any statement to PIX11 News.

And Whole Foods isn’t the only violator in New York City.

Markets in all five boroughs were fined for selling dangerous food. This year alone, owners have been hit with more than 3,000 fines.

But despite how dangerous these conditions can be for your family, inspectors sought to close a miniscule number — just  five stores. Violations  included  mouse and rat droppings.

“Mice can carry a plethora of different diseases,” DeLucia said. “Serious diseases that can affect you and put you in the hospital.”

Inspectors found flies, insects and roaches.

“They can cause asthma the droppings and they are a sign of a filthy place,” DeLucia said.

In Brooklyn, PIX11 investigated one of the borough’s worst offenders. Key Food, with stores in all  the five boroughs, had a disturbing trend.

The chain not only failed 31 inspections in a year, but state inspectors counted up mouse droppings and found more than 2,500 of them.

The East New York store on Rockaway Avenue failed three times in a row, paying $2,400 in fines, but was always allowed to stay open in a neighborhood with few other market options.

Not even two customer complaints to the state about spoiled meat and another that milk purchased there “tasted like chemicals” was enough to close them.

From nesting mice to buzzing flies, mice snacking on food in the flour aisle to hot wings that could give someone a case of food poisoning, we brought in our undercover cameras to see for ourselves.

We quickly found customers clustered around the meat case, upset over the safety of what the store was selling.

“It’s probably old recycled chicken that’s what they’re doing,” one customer said. “I bought a piece of meat, went home something stinking and I’m like, oh my God, I just bought it.”

In all, inspectors fined Key Food for mouse and rat droppings, a mouse nest and two mouse carcasses in the deli, live flies buzzing the produce area and deli and dead roaches in the basement, two dead mice, rice, flour and bread mix that had been gnawed by rodents that had to be thrown out because it’s unsafe for customers, and chicken wings held at temperatures so dangerous that inspectors demanded they be destroyed on the spot.

A manager at the Key Food said he didn’t “know anything about that” but pointed out that the shop passed its latest inspection.

Shoppers we talked to said it’s their long track record of three failed inspections that worries them.

“I bought a loaf of bread here once and the cashier showed me the rodents had been gnawing on it,” said Richard Dove, of Brownsville. “I didn’t even notice and was about to take it home.”

Food expert DeLucia said these filthy conditions can all lead to one terrible fate for customers: “You’re gonna wind up getting sick.”