A series of secondary ion mass spectroscopy (SIMS) analyses of hydrogen, carbon, and oxygen in silicon has been conducted using a magnetic-sector-type SIMS instrument. The effect of energy and angular filtering of secondary ions on the detection limits was investigated in detail. A Cs+ primary beam was used and H-, C-, and O- negative secondary ions were detected with various sample offset voltages and energy window positions as well as contrast apertures in the secondary ion optics. It was found that the lower detection limits can be achieved by offsetting the sample voltage, by translating the energy window toward higher energies, or by using a smaller contrast aperture in the secondary ion optics. These results indicate that most of the background ions from the residual gases have lower axial energy and higher lateral energy relative to the optical axis.