'Unfair' markets only impact day traders: Cramer

Cramer: Don't get lost in HFT weeds

The stock market may be tipped in favor of high-speed traders, but the advantage has minimal effect on retail investors, CNBC's Jim Cramer said Wednesday.

"Look, it's entirely rigged. It's entirely possibly rigged if you trade 50 times a day. These people are going to take a little bit of, a little of your vig," Cramer said on "Squawk on the Street." "If you are out there trying to find the next Google, they're not really going to impact you."

Read MoreSpeed trading like armed robbery without risk: Pro

Cramer criticized high-speed trading for being shrouded in secrecy. He complained the practice is "unfair" to day traders, but added day trading should be left up to the professionals anyway.

"If you're playing this game at home and you're trying to beat these guys, forget it. That's not the right game," Cramer said. "It's not what people should be doing at home."

Instead, Cramer advocated long-term investing., saying people who buy and hold stocks over a long period of time will not see much of an impact from high-speed trading. He recommended investors put their first $10,000 into an S&P 500 index fund and allocate one-quarter of their money for stock picking.

"I think that the market for the last five years proves that if you buy high-quality companies and you hold onto them, you can make a great deal of money," Cramer said.

Cramer hopes the high-speed trading debate won't scare people away from the markets.

"What matters to me is that people not get too caught up in it," he said. "I think it's unfair, but please, don't decide, 'You know what, I'm going to stop looking for Google. I'm not going to find the next Google, I'm going to find a mutual fund and accept the fact that I can do OK.' I think you should do both."

The great debate: Combating HFTs image

Wall Street has been buzzing since publicity surrounding publication of Michael Lewis' new book, "Flash Boys," in which he alleges that high-frequency traders are able to buy stocks ahead of most investors and then sell those shares at a much higher price.

Trading slowed to a near stop on Tuesday as IEX's Brad Katsuyama and BATS Global Markets President William O'Brien engaged in a fiery debate on the subject from the floor of the New York Stock Exchange on CNBC's "Power Lunch."

Read MoreWatch the fight that stopped trading at the NYSE

SEC spokesman John Nester declined to comment on the book, but noted that "The staff, at Chair [Mary Jo] White's direction, is conducting a comprehensive data-driven analysis of a range of market structure issues, including high frequency trading practices and their impact on the fairness, efficiency and integrity of our markets."

—By CNBC's Drew Sandholm.