OBJECTIVES:: To determine the intestinal parasitism prevalence and the relationship between parasite species and hygienic conditions of schoolchildren. METHODS:: This study comprised 61 children (7.77 ± 2.18 years) of a rural school of San Juan, Chimborazo, Ecuador. The participants integrate the EVANES research project and were randomly selected. To determine intestinal parasitism, faeces were analysed. A survey was applied to know the hygienic conditions (water treatment, type of treatment and hand washing) of families and schoolchildren. Data analysis was performed using Chi-square test. Informed consent was obtained and the Helsinki rules were followed. RESULTS::  The prevalence of intestinal parasitism was 93.4%. The parasites identified were cysts of Entamoeba coli (78.7%), Entamoeba histolytica (65.6%), Giardia lamblia (24.6%), Embadomonas intestinalis (19.7%), Chilomastix mesnili (9.8%) and Endolimax nana (13.1%), Giardia lamblia trophozoites (1.6%) and Hymenolepis nana eggs (8.2%). When comparing species according to hygienic parameters, it was observed that the frequency of Embadomonas intestinalis, Chilomastix mesnili and Endolimax nana infections was lower in children of families who treated the water for shower and washed their hands before eating. Hymenolepis nana development was lower in children who drank water treated (boiled, chlorinated, filtered) and use it to shower. CONCLUSIONS:: Schoolchildren of rural highlands have a high prevalence of intestinal parasitism, presenting protozoa and helminths. According to our results, the water treatment may contribute to prevent this pathology.