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 x 10(-7). System improvements could increase the efficiency by many orders of magnitude.