Indonesia carries the heaviest burden of soil-transmitted helminth (STH) infection in Southeast Asia with more than 62 million children requiring preventative chemotherapy in 2017 alone. Prevalence data for many parts of the country are out-dated and knowledge of the risk factors involved in transmission are not clearly understood. The aim of this study was to determine human STH prevalence and knowledge and practices relating to hygiene behaviour in rural communities in Central Java. A cross-sectional survey of 16 villages was conducted in Semarang, Central Java in 2015. Data on demographic, household and knowledge and practices were elicited through face-to-face interviews. Stool samples were collected and examined using the flotation method. Children (2-12 years) also had their haemoglobin (Hb) levels, height and weight data collected, and BMI computed. A total of 6466 individuals from 2195 households were interviewed. One-third of the cohort were infected with at least one species of STH, with differing burdens of the four species identified. Risk of infection was significantly associated with several demographic and household factors. Infection with STH was not associated with negative health impacts (e.g. diarrhoea, low BMI or Hb levels); however rates of anaemia among surveyed 2-12 year olds were high (33%) especially in school-age children. Knowledge of and behaviour related to hygiene and gastrointestinal diseases varied widely and were generally not associated with STH infection. The limited number of associations identified in this study suggests other undetermined risk factors may play a role in STH infection. The study also revealed that STH infection still persists in Central Java despite ongoing deworming programs. Therefore, current control efforts would benefit from being re-evaluated to determine the best way forward.