Children with hemifacial microsomia have a smaller face on the side that is affected. Parents usually note that the corner of the mouth is higher on this side and that the chin does not exactly line up in the middle of the face. The lower jaw (mandible) is flatter and shorter, and the ear is either smaller or not formed at all (microtia). The jaw joint (TMJ) may be small or even completely absent. Some children will have a cleft extending off the side of the mouth (called macrostomia), making the mouth opening larger. Some children will have weakness of the muscles on the affected side of the face. The child's right side is more likely to be affected than the left (2:1), and up to 25% of cases are bilateral (Bifacial Microsomia). Some children are very mildly affected, and others are significantly affected. Intelligence and development are normal.

If a child has a bump, or benign tumor of the eyeball, called an "epibulbar dermoid", then your child may have Goldenhar variant, which may be considered another type of hemifacial microsomia. Children with Goldenhar frequently have fusions of some of the vertebrae (spine) in the neck; however, this almost never requires any treatment.

Craniofacial microsomia is the term given to children with hemifacial microsomia who also have involvement of the upper face and forehead. Typically, the forehead is smaller and is not as far forward that the opposite side. The bones around the eye are usually further back, as well.