vertical CPU

For maximum space usage in my work area, it makes much more sense to sit my CPU on its side, off to the side, rather than have the monitor sit on top of it.  Does this atypical setup present any operating problems?
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Yes you have to take care of your HD. Check the technical description of your HD which side must be down. In general 2 sides are allowed but it depends on your HD. Your CD-drive could be a problem, too.

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We have 3000 PC's here and users put them every way except upside down.  Then only problems we have are when they are placed under the desk and get knocked too hard.
Seagate used to spec that their HD's could operate in any orthogonal orientation except "nose down" as long as they were within 15 degrees of level. Flat, R or L edge should not be a problem.

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