Introduction: Environmental enteric dysfunction (EED) is relevant in public health as it is a potential cause of child stunting. In the Philippines, stunting affects 33.4% of children in 2015. As of date, no local studies on EED exist. This study primarily aimed to determine the prevalence of EED, soil transmitted helminthiasis (STH) and stunting; and their relationships. Methods: A cross-sectional study was conducted among 120 children aged 36-59 months old in Quezon Province, Philippines. EED was assessed via glucose hydrogen breath test with a cut-off of >20 ppm over baseline by 90 minutes suggestive of small intestinal bacterial overgrowth (SIBO), a biomarker of EED. Kato Katz Technique was used to determine STH. Stunting was determined using the 2006 World Health Organization Child Growth Standards. Descriptive and correlation analyses of data were done at 10% level of significance. The study received approval from the National Ethics Committee of PCHRD-DOST, Philippines. Results: Data on expired hydrogen level of <20ppm were documented. The prevalence of STH among children were 38.1% for Ascaris lumbricodes, 15.3% for Trichuris trichiura, and 1.7% for hookworm infections. A high rate of stunting at 40.0% was observed. There was a significant positive association between stunting and the presence of Ascaris (p=0.01). Conclusion: There was no case of EED detected in the study. The severity of stunting was high at 40.0%. Among the STH, the prevalence of 38.1% children having Ascaris lumbricodes was alarming in terms of morbidity control. Nutrition interventions including WASH practices and the use of anthelminthic drugs need to be intensified to address stunting and STH.