BackgroundOver 80% of morbidity due to soil-transmitted helminthiasis (STH) occurs in low-income countries. Children under 5 account for 20–30% of the burden in endemic areas. This study assessed the prevalence, intensity and factors associated with STH infections among preschool-age children (PSAC) in Hoima district, Uganda. The PSAC are particularly vulnerable because the chronicity of this condition usually affects their physical and mental growth and development.MethodsA cross-sectional study was carried out among 562 PSAC (1–5 years old) in 6 counties of Hoima district using Expanded Program on Immunization (EPI) method. Stool samples from children were examined using the formol ether concentration technique for STH egg detection. Egg counts were represented as egg per gram (EPG). A structured questionnaire was used to collect information on factors associated with STH infection. Generalized linear models were used to analyze relationships between STH infection and associated factors.ResultsOverall STH prevalence was 26.5%. Hookworm infection was the most prevalent (18.5%), followed by A.lumbricoides (9.8%) and T.trichiura (0.5%). Prevalence of STH infection was significantly higher in children aged 5 years (Pearson chi-square test, p = 0.009) than in children aged 1 year. The general geometric mean (GM) counts for Hookworm infection was (696.1 EPG; range (530.3–913.8)) with girls having a higher GM (789.8 EPG; range (120–13,200)) than boys. Eating uncooked or unwashed vegetables (adj. Prevalence Ratio (PR) = 1.9, 95% CI: 1.3–2.7) and fruits (adj.PR = 1.8, 95% CI: 1.1–2.8), indiscriminate disposal of young children’s faeces (adj.PR = 1.5, 95% CI: 1.1–2.0); not washing hands after defecation (adj.PR = 2.6, 95% CI: 1.9–3.6); and not deworming children regularly (adj.PR = 1.4, 95% CI: 1.1–1.8) were significantly associated with STH infection.ConclusionThe prevalence of Soil transmitted helminths infection among preschool-age children in Hoima district significantly increased with age. Poor hygiene, inadequate sanitation and irregular deworming were associated with STH infections among PSAC in the study area. Intense health education on the importance of hygienic practices, improved sanitation and regular deworming of PSAC should be integrated into prevention and control programs.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3289-0) contains supplementary material, which is available to authorized users.