The H3+ and H2D+ ions are important probes of the physical and chemical conditions in regions of the interstellar medium where new stars are forming. This paper reviews how observations of these species and of heavier ions such as HCO+ and H3O+ can be used to derive chemical and kinematic properties of nearby pre-stellar cores and the cosmic ray ionization rate towards more distant regions of high-mass star formation. Future prospects in the field are outlined at the end.