Young adult women have had the greatest increase in prevalence of metabolic syndrome (MetS) over time, and prevalence is highest in Hispanic women, compared with women of other ethnicities. Factors contributing to the high prevalence of MetS in Hispanic women are unknown. This study was conducted to determine if physical activity or fitness were associated with individual features of MetS in young Mexican and Mexican-American women, and if the associations were independent of fat mass. Sixty young Mexican and Mexican-American women participated in the study. MetS was defined according to the Adult Treatment Panel III. A fasting blood sample was drawn for the measurement of glucose, insulin, high-density lipoprotein cholesterol (HDL-c), and triglycerides. Physical activity was assessed by questionnaire and accelerometer. Fitness was assessed by progressive treadmill test to exhaustion and ventilatory threshold. Body composition was assessed with Bod Pod. Multivariate regression was used to establish the independent contributions of physical activity and fitness to the individual features of MetS. After controlling for fat mass and fat-free mass, physical activity was found to be independently related to HDL-c and fitness was found to be independently related to triglycerides (p < 0.05). The independent associations between physical activity, fitness, and features of MetS were mediated by, rather than independent of, fat mass. Fat mass was independently related to triglycerides, systolic blood pressure, and diastolic blood pressure. Although physical activity and fitness were related to features of MetS, these associations were not independent of fat mass.