Intestinal helminth infections are highly prevalent and the most public health problems in sub-Saharan Africa including Ethiopia. Children living in area where there is lack of safe water supply, poor personal and environmental hygiene are at increased risk of parasitic infections. A cross sectional study is designed to determine the prevalence of intestinal helminthes and their risk factors among school children in Wogeda town, Wogeda Elementary and Junior Secondary School children from November 2013 to February 2014. A total of 403 stool samples will be collected using systematic random sampling technique. Stool samples will be examined microscopically using direct saline wet mount and formol-ether concentration technique for the presence of parasite eggs, cysts and trophozoites. Interview and structured questionnaire will be used to gather students’ background. Data collected will be analyzed using SPSS version 16 software. Pearson’s correlation and chi-square will be used to analyze the association between intestinal parasites with different demographic variables and risk factors.