The Atom possesses the power to alter his size down to the subatomic level while retaining his natural strength level. This is accomplished by using the remnants of a white-dwarf star made into a belt buckle worn with his costume. Originally, he had to manipulate his abilities via the belt and later with hand movements before eventually syncing with his brainwaves itself. The Atom is one of the few heroes in the DC Universe that has 100% control over his body on the molecular level (Plastic Man and The Flash being examples of others), thus making him exponentially more powerful than he is often portrayed; he is only limited by his application of his powers. Some of the applications he's demonstrated include reducing his mass to glide through the air (simulating flight, like Wonder Woman) and increasing his mass to punch through concrete. He's also demonstrated the ability to make his costume appear and disappear at will by shifting its atoms between this dimension and another.
He has been shown to be able to ride phone lines to his destination by dialing a number and traveling through the handset (his signature use of his power), and recently shrinking small enough to travel on photon signals through fiber optic cable.
Some of The Atom's more impressive feats include shrinking into Superman's bloodstream and manually rearranging his molecules to create Kryptonite and defusing Black Lantern Al Pratt's Atomic Punch and resizing within him, ripping his body apart in the process.
Following the events of Zero Hour, the Atom gained the ability to also grow in size and internalizes his other abilities without the use of his white dwarf star-based apparatus. However, when returned to his natural age, these abilities were lost.
He was a member of the Indigo Tribe, Ray possessed an indigo power ring powered by compassion, which provided him with flight, energy projection, and a protective force field. He also utilised a staff capable of duplicating the abilities of other wielders of the Emotional spectrum within range.
He has also shown the ability to allow others to shrink down with him if the situation requires it, such as when he shrunk himself, Superman, Flash, Green Lantern, Wonder Woman and Plastic Man to repair the links between seven shattered subatomic particles, or shrinking Steel, Supergirl and Superboy to directly treat a kryptonite tumor in Superman's body. However, this ability is relatively limited; initially anyone other than himself who was shrunk would explode after two minutes if not returned to their normal size, although he was later able to extend this time to around an hour.