The Nihilanth is a member of a powerful species that hailed from beyond the Xen dimension, on their own homeworld in their own universe, long before the Black Mesa Incident. In addition, the Nihilanth also wears metallic wristbands similar to those worn by enslaved Vortigaunts. It has unusually long arms, huge hands, and disproportionate fingers.
Underneath its third arm is a surgical scar that goes down its abdomen, which may very well have been a result of experimentation from the Combine. Like all of the other sapient Xen species, it has 3-fingered hands, multiple eyes, and a third appendage protruding from the middle of its chest. Its head is so large that it must be kept upright with a small cord/string that extends from the base of the spine to the back of the head. The creature's minuscule legs appear either to be vestigial or the remains of amputation, as the Nihilanth relies on a levitation device for movement.
Physically, the Nihilanth resembles a gigantic, abnormally proportioned brownish-gray (pink in some lighting instances) fetus with a massive head atop a smaller body.