Background: Intestinal parasitic infection is important public health problem in developing countries. Present study was conducted to identify the prevalence of intestinal parasites and risk factors among children upto age of 12 years hospitalized with diarrhea in tertiary care hospital. Methods: Total 298 children upto the age of 12 years except neonates, admitted in ward of pediatric department with complaints of diarrhea during one year period from May 2011 to April 2012 were included in this study. Various demographic and clinical characteristics were collected on a pretested proforma. Stool smears were examined under light microscope with direct saline smear and lugol`s iodine solution. Parasitic detection was confirmed by formalin ethyl acetate concentration method. Results: Prevalence of intestinal parasites was 8.7% reported among admitted children. Most common parasite isolated was Giardia Intestinalis (5.4%) followed by ascaris lumbricoids (1.3%). Half of study participants were male and belongs to lower socio-economic class. Toilet facility was not available for 26.8% children; 81.2% children received piped water supply of municipality. Duration of diarrhea for more than seven days (p=0.004, OR=4.50, CI=1.59-12.67), more than ten passage of stool per day (p=0.016, OR=2.76, CI=1.20-6.34), non availability of toilet facility (p=0.007, OR=3.05, CI=1.35-6.92) reported as risk factor for intestinal parasitic infection. Such children are more likely to present with vomiting (p=0.038, OR=2.89, CI=1.06-7.90) and abdominal pain (p=0.013, OR=0.35, CI=0.15-0.80). Conclusion: Low socio-economic status, longer duration and frequency of diarrhea, non availability of toilet facility and presence of dehydration were leading risk factors for parasitic infection in present study.