Here's Silicon Valley's answer to the FDA

Not all protein powders or vitamins are created equal, according to San Francisco start-up LabDoor.

In fact, some protein powers contain twice the amount of sodium listed on labels, and some chew-able vitamins contain less than 40 percent of their labeled nutrients, LabDoor CEO Neil Thanedar told CNBC on Wednesday. That's why Thanedar founded LabDoor two years ago—to give consumers an idea of what's in their supplements, and as a result, more purchasing power, he said.

"The market has grown eight times in the last 20 years," Thanedar said on "Squawk on the Street." "That's made it difficult for the FDA and other organizations to really keep track of the industry and that's where LabDoor comes in."

Read MoreSpike in harm to liver is tied to dietary aids

According to the Food and Drug Administration website, dietary supplement manufacturers must register their facilities with the FDA, though their products do not need FDA approval. Thanedar said his company takes products off the shelves as a regular shopper would, and then reverse engineers them through an FDA-approved lab.

The company ranks each product based on its nutritional value, efficacy and purity. They rate protein powers, multivitamins, energy drinks, fish oil capsules and vitamin D supplements. LabDoor also allows shoppers to buy products through its website.

As of now, Carlson Labs' Super 2 Daily vitamins have taken the top spot in the multivitamin section. Chewable vitamins routinely score on the bottom of the barrel, Thanedar told CNBC.

—By CNBC's Jeff Morganteen.