Secondary ion mass spectrometry (SIMS) with argon beam has been used to determine the depth profile of ultra-thin Ti/Si multilayer system deposited on crystalline silicon wafers by laser ablation of titanium and silicon targets. The redistribution of elements in the structure has been studied after subsequent high temperature (HT)-treatment, what leads to uniform metastable phase of the composite films. The data obtained by positive atomic ion detection generated from sample before HT process show anomalous behavior of titanium distribution. We discuss the influence of contaminations on the results and attribute apparent Ti + signal in Ti/Si-based films to numerous ion mass interferences and matrix effects present during sputtering of the multilayers. The negative SIMS analysis in conjunction with detection of sputtered TiO 2 − and Si 2 − molecular species is proposed for depth profiling of Ti/Si to avoid artifacts in Ti and Si profiling, respectively, caused by the presence of contaminations in the multilayers.