The clinical effects of a patient-operated system of microwave disinfection for soft contact lenses were assessed in a prospective pilot trial involving 103 patients who were drawn from five optometric practices. Fifty-six subjects used the test system for 1 month, and 13 subjects continued use for a total of 3 months. Both test and control subjects were examined for clinical signs using slitlamp tests. After 1 month, the incidence of all signs reported in the microwave group was not significantly greater than in the control group (p = 0.267), and the same was true after 3 months (p = 0.214). There was a significantly greater incidence of edema in the 1-month test group and of staining in the control group. UV spectroscopic examination of worn lenses from test subjects exhibiting significant signs did not show a higher level of deposition than on lenses worn by control subjects (p = 0.397)