INTRODUCTION Malaria is a parasitic disease of humans caused by a protozoon of Plasmodium species. Malaria remains to be a life threatening condition and a public health problem in much of Sub-Saharan Africa, it is the most important parasitic disease affecting humans, causing about 1-3 million deaths per year and more than one billion new infections. Despite of the enormous input from various fields controlling Malaria has still not been achieved. OBJECTIVES To assess knowledge, attitude and practices of secondary school students on Malaria prevention in September 2005. METHODOLOGY A cross-sectional study of 398 multistage randomly selected students was conducted in four boarding secondary schools of Morogoro District. RESULTS The study involved 398 respondents. Plasmodium species and mosquito bites were cited as causes of malaria by less than half of students 193 (48.5%) and 172 (43.2 %) respectively. Citing Plasmodium species and mosquito bites as a cause of malaria was significantly associated with level of education of pupils (by X2=22.43, p-value=0.000433 and X2=13.39, p-value=0.02 respectively). Transmission factors mentioned were not using an insect treated bed nets and dirty environment by 91.0% and 77.9% respectively. Mosquito bites were the most mentioned malaria transmission method (97.7%). Students were aware of at least one malaria prevention method 395 (99.3%). 99.0% of respondents used malaria preventive measures with wearing of long clothes and ITN being mostly used by 93.2% and 86.2% respectively. Mass media was a source of information used in more than half of pupils (56.5%). Teachers and mass media as sources of information were significantly associated with pupils level of education (by x2=15.3, p=0.007 and x2=21.2, p=0.0007 respectively) CONCLUSION This study population was aware on methods of prevention of malaria however, the knowledge on the real cause of malaria is low.