Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is an important tool for the analysis of bone minerals at implant surfaces. Most studies have been performed with monoatomic primary ion sources such as Ga+ with poor secondary molecular ion production efficiency and only elemental distributions and minor fragments of bone minerals have been reported. By using cluster ion sources, such as Au and Bi, identification of larger hydroxyapatite species at m/z 485, 541, 597 and 653, identified as Ca5P3O12, Ca6P3O13, Ca7P3O14 and Ca8P3O15, respectively, became possible. The ions appear to be fragments of the hydroxyapatite unit cell Ca10(PO4)6(OH)2. Each ion in the series is separated by 55.9 m/z units, corresponding to CaO, and this separation might reflect the columnar nature of the unit cell. Copyright © 2007 John Wiley & Sons, Ltd.