The cosmic-ray hydrogen and helium ($^1$H, $^2$H, $^3$He, $^4$He) isotopic composition has been measured with the satellite-borne experiment PAMELA, which was launched into low-Earth orbit on-board the Resurs-DK1 satellite on June 15th 2006. The rare isotopes $^2$H and $^3$He in cosmic rays are believed to originate mainly from the interaction of high energy protons and helium with the galactic interstellar medium. The isotopic composition was measured between 100 and 1100 MeV/n for hydrogen and between 100 and 1400 MeV/n for helium isotopes using two different detector systems over the 23rd solar minimum from July 2006 to December 2007.