We have fabricated Se nanoparticles in silica substrates by ion implantation followed by thermal annealing up to 1000°C, and studied the Se nanoparticle formation by optical absorption spectroscopy, Rutherford backscattering spectrometry, X-ray diffraction, and transmission electron microscopy. The sample with the highest dose (1 × 1017 ions/cm2 ) showed the naonparticle formation during the ion implantation, while the lower dose samples (1 and 3 × 1016 ions/cm2) required thermal treatment to obtain nano-sized particles. The Se nanoparticles in silica were found to be amorphous. After thermal annealing, the particle sizes became larger than the exciton Bohr radius for bulk Se. Thus, the absorption edges for different doses approached the value of bulk after thermal annealing. The temperature dependent absorption spectra were also measured for this system in a temperature range from 15 to 300 K.