During the investigation of radioactivity he coined the terms alpha and beta in 1899 to describe the two distinct types of radiation emitted by thorium and uranium. These rays were differentiated on the basis of penetrating power.

From 1900 to 1903 he was joined at McGill by the young Frederick Soddy to collaborate on research into the transmutation of elements.

In 1903, Rutherford realized that a type of radiation from radium discovered (but not named) by French chemist Paul Villard in 1900, must represent something different from alpha rays and beta rays, due to its very much greater penetrating power. Rutherford gave this third type of radiation its name also: the gamma ray.

In late 1907 Rutherford Thomas Royds allowed alphas to penetrate a very thin window into an evacuated tube.

Along with Hans Geiger and Ernest Marsden he carried out the Geiger–Marsden experiment in 1909, which demonstrated the nuclear nature of atoms. It was his interpretation of this experiment that led him to formulate the Rutherford model of the atom in 1911.

In Cambridge in 1919 he became the first person to transmute one element into another when he converted nitrogen into oxygen through the nuclear reaction 14N + α → 17O + p.

In 1921, while working with Niels Bohr (who postulated that electrons moved in specific orbits), Rutherford theorized about the existence of neutrons, which could somehow compensate for the repelling effect of the positive charges of protons by causing an attractive nuclear force and thus keeping the nuclei from breaking apart.

Rutherford's theory of neutrons was proved in 1932 by his associate James Chadwick, who in 1935 was awarded the Nobel Prize in Physics for this discovery.