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I know that sometimes a lens/body combo needs to be micro-adjusted to attain ideal focusing behavior, and that this is usually because of sample variation, but which parts of the lens and/or body are actually the primary causes of front/back focus?

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It can be any number of different things. It all comes down to the tolerences that consumer cameras are built to.

Typical suspects would include:

  • Lens Element locations
  • Flange-to-film distance
  • Sensor location
  • Focus sensor

It is all about the location of the focal plane as outlined here: What is back-focusing?

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