The Mac Pro (2013) has a fan system capable of cooling the computer in a vertical or horizontal orientation as long as you follow these guidelines.It is likely that third-party companies will come out with rack-mount options for the new Mac Pro at some point and those mounts could see the machine aligned on its side in order to maximize space.
- Provide enough space at each end of the computer for unrestricted airflow into the base and out the exhaust at the top. Make sure that the air intake and exhaust ports are not covered.
- When using multiple Mac Pro (Late 2013) computers, do not direct the exhaust at the top of one Mac Pro towards the intake of another system. Place the computers side by side with a gap of at least several inches between them.
- When on its side, secure the Mac Pro (Late 2013) to be sure that it doesn't roll. Place the computer on a protective surface that will not scratch or damage the enclosure. Note: The Apple Limited Warranty does not cover cosmetic damage to the enclosure.
- Orient the computer so that the Input/Output (I/O) panel remains accessible during use.
(Sideways Mac Pro courtesy The Verge)