A polyatomic ion or molecule ion is an ion consisting of covalently bonded atoms that can be considered as acting as a single unit in the context of acid/base chemistry or in the formation of salts. For more information on polyatomic ions containing metals, and how to name these, see metal complex. Note, a polyatomic ion is also referred to in older works as a radical. In current usage the term radical refers to free radicals which are uncharged species with an unpaired electron.

Some commonly-occurring polyatomic ions and their charges are indicated below:

• aluminate Al₂O₄^2-
• carbonate CO₃^2-
• bicarbonate HCO₃^- (more correctly known as hydrogen carbonate)
• tetraborate B₄O₇^2-
• chlorate ClO₃^-
• chromate CrO₄^2-
• cyanide CN^-
• hydroxide OH^-
• nitrate NO₃^-
• nitrite NO₂^-
• permanganate MnO₄^-
• peroxide O₂^2-
• phosphate PO₄^3-
• phosphite PO₃^3-
• pyrophosphate P₂O₇^4-
• silicate Si_xO_y (many varieties, often polymeric)
• sulfate SO₄^2-
• sulfite SO₃^2-
• triflate CF₃SO₃^- (trifluoromethanesulfonate)
• acetate CH₃CO₂^-
• formate HCO₂^-
• oxalate (CO₂)₂^2-
• ammonium NH₄⁺
• quaternary ammonium NR₄⁺
• hydronium H₃O⁺
• pyridinium C₅H₅NH⁺

The atoms of a polyatomic ion are always associated with each other via covalent or coordinate-covalent bonds.

A large polyatomic ion will often be considered as the conjugate acid or conjugate base of a neutral molecule, for example the conjugate acid of adrenaline at the amine group.

Note that many of the common negatively-charged (anionic) polyatomic ions are conjugate bases of acids derived from the oxides of non-metallic elements. For example sulfate or SO₄^2- ion is derived from H₂SO₄ which can be regarded as SO₃ + H₂O.

Bicarbonate is also called hydrogen carbonate in modern chemical nomenclature.