Introduction: Intestinal parasitic infections are an important but neglected health problem especially among children in developing countries. These infections are among the major causes of undernourishment morbidity, impairment of physical and mental development. Aim: The aim was to study the occurrence of intestinal parasitic infection in children of 1 to 15 years of age and their effect on health. Materials and method: A total of 400 stool specimens were collected from the children with gastrointestinal symptoms at Central Refferal Hospital and Sir Thodup Namgyal Memorial Hospital during 2015 to 2017. Stool smears were examined microscopically using direct and after concentrated with saline and iodine mounts. Acid fast stain smears were used to stain Taenia eggs and coccidian oocysts. Agar plate culture techniques were used for hookworm eggs for species identification. Results: The prevalence of parasitic infection was found to be 17.5%. The most common parasites were Giardia intestinalis (5%), followed by Taenia (3.7%) and hookworms (3.5%). Among the Taenia, T.saginata was 15.7% (11/400) and T.solium was 5.7 %( 4/400) and among the hookworms, Necator americanus was 2.8% (11/400), Ancylostoma duodenale was 0.5 %( 2/400) and Strongyloides was 0.2% (1/400). Conclusion: Understanding the occurrence of various intestinal parasitic infections in children in different sectors of the society, localities are very important to develop appropriate control strategies as the frequency of infestation varies with age, sex and different geographical location of the general population.