A study to evaluate the effectiveness of school health education for mosquito borne diseases vector control program was conducted in East Flores Regency, East Nusa Tenggara Province. The method of study include education program for the teachers and 4th through 6th grade students from 2 primary schools and another school in the area was chosen as control. The evaluation was made through responses obtained from the questionaires given before and after the education program for malaria and filariasis regarding their sign, symptoms, the vector and prevention. The results show that there are 3,82% and 4,10% increase in knowledge about malaria and filaria respectively after the education program. This means the education material was well accepted. Although there was an overall increase in knowledge about malaria, no similar response was noted for filariasis. Thus the education material for filariasis should be improved. The result of the study suggest that a continous education program for malaria and filariasis should be incorporated into the regular School Health Education curicullum in the endemic areas.