The Morgan horse is compact and refined in build, with strong limbs, an expressive face, large eyes, well-defined withers, laid back shoulders and a well arched neck and a clean cut head. There is officially one Breed Standard for Morgan type regardless of the discipline or bloodline of the individual horse.

Registered Morgans come in a variety of colors although they are most commonly bay, black, and chestnut. Less common colors include gray, palomino, roan, cremello, perlino, dun, buckskin, and silver dapple. Since a recent registration rule change eliminating rules on white markings, three of the pinto color patterns are also recognized sabino, frame overo, and splashed white. The tobiano pattern has not been noted in Morgans.

The breed standard ranges from 14.1-15.2 hands (1.45 to 1.57 meters) with some individuals over and under. Morgans under 14.2 are eligible for registration with the National Morgan Pony Registry and can be shown in open "Pony" competitions, even though they are technically horses, regardless of height, and are usually exhibited as such.