Introduction: There is a dearth of public health and nutrition information available pertaining to the indigenous groups in the Philippines. Hence, this study described the prevalences of stunting and zinc deficiency, as well as factors associated with zinc status of 3-5 years old children among the Kankana-ey people, an indigenous group living in Kibungan, Benguet, Philippines. Methods: A cross-sectional design was used in the conduct of the study where 63 study participants were randomly selected from a chronological list of names of eligible Kankana-ey children by drawing lots. The mothers/primary caregivers of these children were interviewed to collect their socio-economic and demographic data, and dietary intake was assessed through three non-consecutive days 24-hour food recall. Height and weight of the children were also measured to determine their nutritional status. Lastly, blood samples were collected to determine the zinc status of the children based on serum zinc concentration, analysed through atomic absorption spectrophotometer. Results: Results showed that 54.0% and 50.8% of the Kankana-ey children had stunting and zinc deficiency, respectively. There was significant positive association between being exclusively breastfed and current zinc status (p=0.001). On the other hand, a statistically significant negative correlation was observed between zinc intake and zinc serum concentration (r=-0.291, p=0.021). Conclusion: Undernutrition among Kankana-ey children is a major public health concern in Kibungan, Benguet. Preventive actions must be taken to alleviate the severity of both stunting and zinc deficiency, and to mitigate possible consequences by strengthening the current nutrition and health programmes for indigenous groups, especially among young children.