It may seem like commission checks are taxed at a higher rate then your salary checks because they are usually much larger than the normal paychecks so they fall into a higher tax bracket for the withholding purposes. However, when all your income & withholding from all sources are entered on the annual tax return any over withholding is added to your refund. So it balances out in the end. If your refunds are higher than you like then increase your W-4 allowances so your regular paychecks aren't hit as hard to make up for the commission checks.
