The composition of ternary Si-B-O films some tens of nm thick, which grow during the thermal pre-deposition of boron in silicon, has been determined by X-ray microanalysis. The X-ray intensity data have been obtained by using an automated ARL-SEMQ microprobe operated at 20 kV. The experimental k ratios have been converted into concentrations using a Monte Carlo computer program based on the single-scattering approach. In the case of a film with an underlying substrate, which includes an element of the compound film, an independent determination of thickness is necessary. A general computer analysis on the effect of the substrate on electron trajectories and X-ray yields is performed; the possible sources of error are discussed. The composition of the films so obtained is in satisfactory agreement with the data previously deduced from Rutherford backscattering experiments. This result allows us to solve a discrepancy between the two analytical techniques found before in the case of substrate removal; a variation in chemical composition of the films during the removal of the substrate may be suggested.