Background: Metabolic syndrome (MetS), a prevalent health condition in Taiwan, places individuals at higher risk of cardiovascular disease, diabetes, and stroke. Therefore, the identification of risk factors associated with MetS is crucial. Nevertheless, only limited studies about MetS have been conducted among indigenous peoples in Taiwan; these studies identified a high prevalence of MetS among an indigenous population, which encouraged us to investigate further. Thus, our study aims to determine the prevalence of MetS among the northern Taiwanese indigenous population and to explore the relationship between MetS and associated risk factors, especially serum alanine transaminase (ALT). Methods: This is an observational, population-based, cross-sectional study that was conducted in remote villages of an indigenous community in northern Taiwan between 2010 and 2015. A total of 454 participants, 47.36% male and 52.64% female, were eligible for analysis. The participants underwent anthropometric assessment and measurements of blood pressure, serum triglyceride levels, fasting plasma glucose levels, serum HDL-C levels and serum ALT levels. MetS was defined based on the revised NCEP/ATPIII criteria from Taiwan Health Promotion Administration. Results: A total of 454 participants were included in the analysis. There were 277 people with MetS and 177 people without. The prevalence of MetS was 61.01%. The average age was 49.50 years old. People with MetS had a significantly higher ALT level (24.00 (17-36) U/L vs. 19.00 (15-26) U/L, p<0.001) than those without MetS. In addition, the chi-square comparison showed that participants with ALT levels>36 U/L had a tendency towards a higher prevalence of MetS (76.7% vs. 57.3%, p=0.001) than those with ALT levels≤36 U/L. The adjusted odds ratio (OR) of ALT levels >36 U/L for MetS was 2.79 (95% CI=1.24-6.27, p=0.01). The area under the ROC curve (AUC) of the ALT level was 0.63 (95% CI=0.58-0.68, p<0.001), which showed that the ALT level was positively associated with MetS. Conclusions: The overall prevalence of MetS was 61.01% in the highland indigenous population in Northern Taiwan, which suggests an unignorable health problem that should actively be addressed. Furthermore, these findings indicated that higher serum ALT levels (>36 U/L) were associated with an increased risk of MetS.