The effects of grapefruit seed extract and $H_2O_2$ disinfectants on Pseudomonas aeruginosa were investigated by antimicrobial assay and scanning electron microscopy. Pseudomonas aeruginosa is a Gram negative bacteria and a common causative microorganism of bacterial keratitis. After incubation of soft contact lens in Pseudomonas aeruginosa suspension for 120 minutes containing the disinfectants, the grapefruit seed extract showed antimicrobial activity as good as the chemical disinfectant. The living rates of Pseudomonas aeruginosa in grapefruit seed extract and $H_2O_2$ disinfectants were $1{ imes10^3CFU/m{ell}$ and $0.5{ imes}10^3CFU/m{ell}$, respectively showing no major difference in the killing activity. However, the mechanisms of the antimicrobial activity were quite different as indicated by scanning electron microscopy of the bacterial surface morphology. Considering chemically or other toxins induced keratitis, the natural disinfectant isolated from grapefruit seed extract shows promising results as a soft contact lens disinfectant.