Desktop printers, and many commercial copiers, are not built to the same tolerances as printing presses and front-to-back and page-to-page shifts of up to 1/8" or 3mm are to be expected. There is nothing in InDesign that you can do to change how the printer works, but you can use larger margins to help disguise the misalignments.
How big a misalignment, and what kind of printer? If there are image shift settings in the printer driver, they should be the best way to compensate.
Thanks Peter we were print booklets on 8.5 X 14 paper the misalignment back to front was 0.125 of an inch. How big would you compensate margins we had 1 inch all round?
I would have thought that would be enough...
Are you running through a finisher that folds and staples right on the machine? If not, consider printing the fronts, then reloading the trays and printing the backs. You may get more consistent results that way, or, if the shift seems consistent with the duplexer, you could do a margin shift on the second side pages to move the page image over (see, I lied above about not being able to fix it in ID, but only a little -- it depends on how consistent the printer shift actually is), then print a PDF from Acrobat instead of using Print Booklet in ID.
Back in the dark ages when I worked for a service bureau I set up a two-page file with center lines and marks at about 4 pts spacing for a half inch either side of both horizontal and vertical center lines and at the page edges, then printed it a few times duplexed and re-fed thought the bypass tray on the Xerox copier to get a sense for the consistency. To check the drift you can look at what gets cut off at the edges (count the lines) or fold the sheet and check how far off the center lines are.