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BackgroundEnteric pathogens contribute to child malnutrition in low-to-middle-income countries. In Timor-Leste, there has been limited study of this relationship.Methodology/Principal findingsWe investigated enteric disease, stunting, and malnutrition in children in Dili, Timor-Leste (July 2019 – October 2020). Sixty infants received up to four home visits. We collected faecal samples, demographics, anthropometrics, food and water sources, feeding practices, and animal husbandry details. For 160 children admitted to Hospital Nacional Guido Valadares with clinical diagnosis of severe diarrhoea or severe acute malnutrition (SAM), we collected faecal samples, diagnostics, and anthropometrics. Faeces were tested by polymerase chain reaction (PCR) using the BioFire®FilmArray®Gastrointestinal Panel. Descriptive analyses and regression analyses were conducted using R.We detected enteric pathogens in 68.8% (95% confidence interval [CI] 60.4–76.2%) of infants, 88.6% of children with SAM (95% CI 81.7–93.3%), and 93.8% of children with severe diarrhoea (95% CI 67.7– 99.7%). DiarrhoeagenicEscherichia coliandCampylobacterspp. were most frequently detected. A median weight-for-height Z-score (WHZ) of -1.1 (interquartile range [IQR] -2.0 to -0.1) for infants across all home visits, -3.9 (IQR -4.7 to -3.0) for children with SAM and -2.6 (IQR -4.2 to -1.1) for children with severe diarrhoea was observed.The most common admission diagnosis was SAM (88.1%, 95% CI 81.7–92.5%). Hospitalised children had increased odds ofShigella/enteroinvasiveE. coli(OR 11.4, 95% CI 2.8–47.3) andGiardia lambliadetection (OR 31.7, 95% CI 3.6–280) compared with infants. For home visits, bottle feeding was associated with increased odds of pathogen detection (OR 8.2, 95% CI 1.1–59.7).Conclusions/SignificanceWe detected high prevalence of enteric pathogens and signs of malnutrition in children in Dili. Our pilot is proof of concept for a study to fully explore the risk factors and associations between enteric pathogens and malnutrition in Timor-Leste.Author summaryEnteric pathogens are a contributing factor to child malnutrition in low-to-middle-income countries. This study investigated the relationship between enteric disease, malnutrition, and stunting in children in Dili, Timor-Leste. Sixty infants received up to four home visits and 160 children were admitted to the hospital with a clinical diagnosis of severe diarrhoea or severe acute malnutrition. Faecal samples were collected and tested for enteric pathogens and risk factors were explored. The study found that enteric pathogens were detected in most infants and children with malnutrition and diarrhea. The most commonly detected pathogens were diarrheagenicEscherichia coliandCampylobacterspp. Most children exhibited signs of malnutrition from infancy, and hospitalised children had a higher likelihood of having certain enteric pathogens. Feeding practices, water use, and animal cohabitation may pose risks for enteric pathogen infection. The results suggest that enteric pathogens are a significant problem in Dili, Timor-Leste, and further research is needed to explore the complexity of risk factors.