It's natural to compare online brokers based on their commissions.

After all, the whole discount brokerage industry was founded on the principal of lower commissions.

But as the number of online brokers has grown, so too has the complexity of pricing.

Indeed, that deeply-discounted flat-rate commission you see advertised on an online broker's web site isn't necessarily the one you'll pay.

And depending on the online broker and the type of trades you make, you may pay far more in fees than you do in commissions. (See also: “Hidden Fees Your Broker Won’t Tell You About.”)

How You Plan to Trade Makes a Difference

When the vast majority of brokers quote a flat rate commission, they're doing so for trades that are executed online.

Those same online brokers will charge higher commissions for automated trades that are done by touch-tone telephone, or broker-assisted trades.

TD Ameritrade, for example, advertises commissions of $9.99 no matter how many shares you buy. But that same trade will set you back $34.99 if use Ameritrade's automated touch-tone telephone service and $44.99 if you use a broker to help.

An exception: TradeKing charges $4.95 for equity trades, whether executed online or with the assistance of a broker. But TradeKing is not going after investors who want to execute trades with a broker on a regular basis.

"That's an accommodation we make to our clients out of respect for them," says TradeKing CEO Don Montanaro. "There are situations where our clients are not able to be in front of a computer. They don't want to be penalized for that."

What You're Buying Matters

Buying and selling stocks? Fine. You may get the advertised commission (assuming you qualify for it in every other way). But don't expect that to hold true if…

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