Vanguard took the ETF fee war to a whole new level after announcing the switch to FTSE and CRSP indices from MSCI benchmarks. Now, investors will have to brace for potential changes and the effects on their portfolio allocations.

In a related move, BlackRock (NYSE: BLK) recently lowered expense ratios at six of its iShares funds. It also launched the new iShares Core Series targeting long-term investors. [The Phony ETF Fee War?]

Vanguard will be switching out the benchmarks on 22 of its index funds. The largest funds to swap out their index include the Vanguard Emerging Markets Index (NYSEArca: VWO), which will track the FTSE Emerging Index, and the Vanguard Total Stock Market (NYSEArca: VTI), which will follow the CRSP Total market Index, Dan Culloton, associate director of fund analysis for Morningstar, said. [Vanguard Benchmark Trade Shakes Up Index Industry]

While retail investors may be unfamiliar with the CRSP brand, the index provider, which is based out of the University of Chicago Booth School of Business, has been around since 1960 and is well known among academic financial circles.

CRSP’s methodology also differs slightly from MSCI’s approach.

“They use a different method of moving stocks across market cap and style boundaries in their indexes–where it’s more gradual and allows for stocks to be held in more than one index at a time, which could reduce turnover over time,” Culloton said. “They add some, I guess you would call them, earnings quality metrics, such as looking at current assets and return on assets in their growth factors, which could also have a difference in exposures over time. ”

“CRSP breaks up its market-cap boundaries by a percent of market cap,” Culloton added. “So its large-cap index, instead of being the 750 largest stocks, would be the top 85% of the market.”