Research on associated risk factors for intestinal parasitic infections and malnutrition in various geographic regions is needed for the development of appropriate control strategies. The aim of this study was to determine the risk factors associated with intestinal parasitic infections, anaemia, and malnutrition in school children, living in urban and rural areas of northern Ethiopia. Six hundred school children, aged 6-15 years, were randomly selected in a cross-sectional survey from 12 primary schools. Sociodemographic and anthropometric data were collected. Faecal samples were examined using direct, concentration, and the Kato-Katz methods. Urine specimens were analysed for Schistosoma haematobium ova. Haemoglobin was measured using a HemoCue spectrometer. The overall prevalence of intestinal parasitosis was 72% (95% confidence interval (CI): 66-76%). The prevalence of anaemia, stunting, and thinness were 11% (95% CI: 8-13%), 35% (95% CI: 31-38%), and 34% (95% CI: 30-38%), respectively. Poor personal hygiene habits were generally associated with anaemia and nutritional deficiency (low body mass index). Multivariate logistic regression models related Schistosoma mansoni infection with boys. Boys were also more likely to be malnourished. Hookworm infection was associated with anaemia and unhygienic finger nails. Access to clean water and latrines, with some hygiene and sanitation communication activities, could improve health of children in Ethiopia. The use of smartphone technology in demographic data collection proved to be successful. The potential advantage offered by this technology for parasitological field surveys merits further investigation.