Laser manipulation of neutral atoms has been used to count individual krypton-85 and krypton-81 atoms present in a natural krypton gas sample with isotopic abundances in the range of 10 −11 and 10 −13 , respectively. This method of isotope trace analysis is free of contamination from other isotopes and elements and can be applied to several different isotope tracers for a wide range of applications. The demonstrated detection efficiency is 1 × 10 −7 . System improvements could increase the efficiency by many orders of magnitude.