You need to loop thru all the repeater's items, test for the right item types then you can find the checkbox control and set its checked property.
For Each objItem In objCountyRepeater.Items
Select Case objItem.ItemType
Case ListItemType.AlternatingItem, ListItemType.Item, ListItemType.SelectedItem
objCheckBox = CType(objItem.FindControl("cbxSelected"), CheckBox)
If Not objCheckBox Is Nothing Then
objCheckBox.Checked = False
End If
End Select
Next
Here's a working example. You can see the code for it there as well.
http://www.geekdork.com/samples/repeaterCheckboxes.aspx
Peter
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Work smarter, not harder.