Recently, various bio-medical applications of nanoporous silicon (np-Si) have been suggested. This work investigates the biocompatibility of np-Si particles taking into account hazardous residua confined in the pores after preparation. The emphasis is on the potential application of such particles as oxygen photosensitizer for photodynamic therapy of cancer, which requires both negligible toxicity of np-Si particles in darkness and a high photo-cyto-toxic effect due to generation of singlet oxygen under illumination. Considerable amounts of water soluble toxic impurities are found to be present in the nanoporous shell of micrometer-sized np-Si particles immediately after their preparation by chemical etching of bulk silicon powder. The effects of several ordinary cleaning treatments are investigated by using thermal effusion mass-spectroscopy and FTIR spectroscopy. A particular purification procedure is developed, capable to reduce the concentration of residual impurities to levels acceptable for bio-medical applications while preserving the required photo-activity of the np-Si particles.