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Background  Parasitic infection is the most prevalent among rural communities in warm and humid regions and where water, hygiene and sanitation facilities are inadequate. Such infection occurs in rural areas where water supplies are not enough to drink and use, and in the absence of environmental sanitation, when the rubbish and other wastes increased, and sewage and waste water are not properly treated. Hence the aim of the study was to assess the prevalence of intestinal parasitosis and associated risk factors.    Methods  This cross sectional study was conducted on children of the selected primary schools in Chencha town from March to May, 2012. Children were selected within age group 5–15 years. The socio-demographic, environmental and behavioral variables data were collected using structured questionnaire from the guardians of children and school teachers to assess the risk factors. Prevalence of intestinal parasitosis was determined using direct method and formol-ether concentration method. Participants’ data were analyzed using SPSS version 16.0.    Results  Of 422 selected school children, 400 participated in the study with full information for analysis. The overall prevalence of intestinal parasitosis was high (81.0%). Soil-transmitted helminths (STHs) infections (63.0%) were more prevalent than protozoa infections (23.5%). The predominant parasites were  A.lumbricoides  (60.5%),  E.histolytica/dispar ( 16.25%),  Giardia lamblia ( 11.7%) and  T.trichuria  (9.7%). The presence of Intestinal Parasitic Infections (IPIs) have statistically significant association with the educational status of the household heads, absence of washing facility, home cleanness condition and type of latrine used with (p < 0.05).    Conclusions  The prevalence of intestinal parasitic infections, especially soil-transmitted helminths (STHs) is very high in the school children. The high prevalence of parasitic infections in these children indicates that the protozoa and helminths concerned are very common in the environment of these villages and the results of the risk factors analysis suggests that the transmission is from several routes. Therefore, multiple intervention strategies should be implemented for the school children, households and the environment to reduce the disease burden.

Assessment of the prevalence of intestinal parasitosis and associated risk factors among primary school children in Chencha town, Southern Ethiopia