New low cost and accurate estimation method of transformer stray capacitances for wide band DC-DC converter modelling and design is proposed. The Wiener filter (WF) method is applied to estimate the transformer impedancereferred to the selected transformer winding configurations. Laboratory tests are used to adapt the filter, that is to find optimal impedance which minimises mean square error between measured, noise perturbed current and reconstructed current. Transformer transfer function peaks indicate internal LC resonances. Stray capacitances are extracted based on resonant frequencies determination. The method validation is carried out by simulation and experimental analysis, where estimated stray capacitances by WF are compared with measurements of an impedance analyser.