First determine whether the amount is significant. If the answer is yes, the best method for finding errors is to review each item marked cleared in QuickBooks with the transactions listed on your bank statements.
If the difference shown on the Reconcile – Account dialog is not significant, you can reconcile with an adjustment, as in the example below.
Click to enlarge:
Clicking Reconcile Now will create an adjustment transaction.
QuickBooks places this adjustment amount into an automatically created Expense account called “Reconciliation Discrepancies.” See the section titled “Reconciling with an Adjustment,” in Chapter 6 of the QuickBooks 2010 Solutions Guide
From Laura Madeira’s QuickBooks 2010 Solutions Guide