We present new Isotope Dilution Thermal Ionisation Mass Spectrometry (ID-TIMS) U-Pb reference ages for apatites from type locations Durango, Cerro de Mercado, Mexico and Wilberforce, Ontario, Canada. A weighted mean 206Pb/238U obtained from 14 Durango apatite fragments yields an age of 32.716 ± 0.061/0.063/0.072 Ma (2σ analytical uncertainty; analytical and tracer uncertainty combined; analytical, tracer, and decay constant uncertainties combined; MSWD = 0.81). Correction of excess 206Pb from Th-disequilibrium in Durango apatite, using a Th/Umelt of 3.5 ± 1, yields a weighted mean 206Pb/238U age of 32.29 ± 0.12/0.12/0.12 Ma. A concordiaconstrained linear 3-D isochron yields an age of 32.683 ± 0.050 Ma for Durango apatites (ratio + error (%) + correlation coefficients; MSWD = 7.6; no propagation of decay constant and Pbc composition uncertainty, isoplot v. 4.15). A weighted mean 206Pb/238U obtained from 9 Wilberforce apatite fragments yield an age of 930.9 ± 8.0/8.0/8.1 Ma (MSWD = 0.65). Excess 206Pb correction for Wilberforce is negligible (<100kyr) relative to the uncertainty. A concordia-constrained linear 3-D isochron yields an age of 923 ± 14 Ma (ratio + error (%) + correlation coefficients; MSWD = 367; no propagation of decay constant and Pbc composition uncertainty, isoplot v. 4.15) for Wilberforce apatites. Initial Pb isotope compositions for these apatites were obtained by regression of the U-Pb data (3-D linear regression) and yielded a 206Pb/204Pb of 18.19 ± 0.12 and 207Pb/204Pb of 15.67 ± 0.10 for the Durango apatite reference material, and a 206Pb/204Pb of 17.06 ± 0.37 and 207Pb/204Pb of 15.33 ± 0.29 for the Wilberforce apatite reference material. Varying the assumed initial Pb composition can have significant effects on the calculated U-Pb age of apatites, which is highlighted with synthetic apatite data based on the composition of the Durango apatite reference material. For Durango apatites, the frequently used estimates of common Pb from two-stage Pb evolution models can artificially shift the U-Pb data and yield inaccurate dates, relative to the use of 3-D isochrons constructed using data obtained from Durango apatite. The use of 3-D isochrons to extract initial Pb isotope data should be restricted to samples/material with single U-Pb date population (closed system) and where estimates from Pb-bearing-U-free co-genetic mineral phases is unavailable and evaluated on a case-by-case basis.