Hyperfine structure is a small perturbation in the energy levels (or spectral) of atoms due to the proton-electron dipole moment interaction. The amount of correction to the Bohr energy levels due to "hyperfine splitting" is on the order of:

where m is the mass of an electron, m_p is the mass of a proton, α is the fine structure constant (1/137.036), and c is the speed of light. This is a much smaller perturbation than the fine structure or Lamb shift.

Also hyperfine structure gives the 21 cm line observed in HI region in interstellar medium.

Use in defining the SI second

The hyperfine structure transition can be used to make a microwave notch filter with very high stability, repeatability and Q factor, which can thus be used as a basis for very precise atomic clocks. Typically, the hyperfine structure transition frequency of a particular isotope of caesium or rubidium atoms is used as a basis for these clocks.

Due to the accuracy of hyperfine structure transition-based atomic clocks, they are now used as the basis for the definition of the second. One second is now defined to be exactly 9,192,631,770 cycles of the hyperfine structure transition frequency of caesium-133 atoms.