In high mass resolution secondary ion mass spectrometry Cs+ depth profile measurements of Si in GaN films, the secondary ion intensity ratio of Si-28(-) to the matrix Ga-69(-) signal has been observed to be poorly repeatable from measurement to measurement. In some cases the Ga-69(-) signals from adjacent areas showed different intensity levels even though the Si-28(-) intensities were similar. Variation of the Ga-69(-) matrix signal from run to run creates a large uncertainty in the determination of the Si concentration in a GaN film when a relative. sensitivity factor is used. The changes in Ga-69(-) intensity from repeat measurements have been determined to be affected by the instrument vacuum condition, ion energy distribution, sample charging, and type of sample holder used in the measurement.