Heterogeneous concentrations of α-producing nuclides in apatite have been recognized through a variety of methods. The presence of zonation in apatite complicates both traditional α-ejection corrections and diffusive models, both of which operate under the assumption of homogeneous concentrations. In this work we develop a method for measuring radial concentration profiles of 238U and 232Th in apatite by laser ablation ICP-MS depth profiling. We then focus on one application of this method, removing bias introduced by applying inappropriate α-ejection corrections. Formal treatment of laser ablation ICP-MS depth profile calibration for apatite includes construction and calibration of matrix-matched standards and quantification of rates of elemental fractionation. From this we conclude that matrix-matched standards provide more robust monitors of fractionation rate and concentrations than doped silicate glass standards. We apply laser ablation ICP-MS depth profiling to apatites from three unknown populations and small, intact crystals of Durango fluorapatite. Accurate and reproducible Durango apatite dates suggest that prolonged exposure to laser drilling does not impact cooling ages. Intracrystalline concentrations vary by at least a factor of 2 in the majority of the samples analyzed, but concentration variation only exceeds 5x in 5 grains and 10x in 1 out of the 63 grains analyzed. Modeling of synthetic concentration profiles suggests that for concentration variations of 2x and 10x individual homogeneous versus zonation dependent α-ejection corrections could lead to age bias of >5% and >20%, respectively. However, models based on measured concentration profiles only generated biases exceeding 5% in 13 of the 63 cases modeled. Application of zonation dependent α-ejection corrections did not significantly reduce the age dispersion present in any of the populations studied. This suggests that factors beyond homogeneous α-ejection corrections are the dominant source of overdispersion in apatite (U–Th)/He cooling ages.