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I recently purchased a Canon 100-400mm L IS lens to use with my 5D MKII and have been using it trouble free off and on for a couple of weeks.  Today I was out shooting a marathon with it.  The shots were looking great but I decided to put a polarizer on the lens to cut down on some glare as the sun moved across the sky.  As soon as I did, the focus on all the images degraded dramatically.  I was shooting in shutter priority mode so the only camera setting that changed was the camera picked a more open aperture (typically from about f11 to about f5.6) to make up for the reduced light through the filter.

I've used this same filter on my usual lens (24-105 mm L IS) and never saw this issue with focus before.

As soon as I took the polarizer off the images came out perfectly sharp again.  I checked to make sure the filter was clean before I put it on the lens and I checked it again when I took it off.

I've never seen this type of behavior before.  Anybody have any ideas why this might happen?

Thanks!

Is it the f-stop or the filter? The 100-400 is not the sharpest lens in the world, shooting at 400mm you may find that anything under f/8 (hypothetical example) will start to look soft. The filter just forced you to open up.

You can test the theory by shooting some pictures, of the same scene, at 400mm; at ISO 800, then ISO 400, 200 and 100. That will force the lens to open more for each successive shot. Everything else is the same, a controlled experiment.

The ISO 100 photos should be sharper, but if the lens is getting noticeably softer at wider openings you have your answer.

My guess. My 100-400 is sometimes just fine and sharp and other times I wonder what is wrong with the lens or the camera. Longer focal lengths, lets say 360 and above, can result in out of the ordinary soft shots.

But then he didn't have the problem in the 24-105...

I think Race's answer for a quality drop due to larger aperture makes sense.

Yes, it was a circular polarizer.

I was shooting at ~200 mm.

Perhaps it's just the aperture change at longer focal lengths but the focus problem was pretty pronounced and much more than I've seen on the lens before.  I'll play around with it at different ISOs as suggested and see what happens.

Thanks!

Unless there is some live-view thing going on the aperture should be wide open while the camera is focusing.(?)

so you were struggling to get an AF lock with the filter? or just looking at the results you can see the difference?

I'd expect AF to sometimes miss or hunt a little longer on an dull day with a long lens and filters, but you say it was sunny. strange. my first though also was linear polariser. you could do some trials with a neutral density filter and see if the same happens.

If you've gone from f11 to f5.6 then you have significantly reduced the depth of field which gives a smaller margin of error, important with a moving subject.

Were the runners coming towards you at relatively short range when you had the issue? I have found that even in AF Servo mode that lens can struggle to keep up and adding the polarizer would obviously make the problem worse.

Was the IS set to the correct mode for what you were shooting (Set 2 for panning)?

The more light and the higher shutter speed the better for that lens, or any other zoom telephoto. I'd avoid using a polarizer as any gains from reduced glare will be offset by reduced lens performance.