Background Metabolic syndrome (MetS) risk factors have been reported in Uganda, yet, the role of dietary factors of MetS, such as fruit and vegetable (FV) intake is rarely reported. Objective To examine the association between fruit and/or vegetable intake and MetS risk factors in Ugandan adults aged 18-69 years. Methods In this cross-sectional study, data from the 2014 Uganda non-communicable disease risk factor survey was analyzed. The mean intake of fruits and/or vegetables according to the number of MetS risk factors, and the odds ratios of each risk factor according to quartiles (Q) of fruits and/or vegetable servings were computed. Results Overall, 1,396 men and 1,736 women were analyzed. Mean age was 34.4 years, mean daily servings of total FV was 2.6±0.1, and 77.7% of participants were diagnosed with at least a MetS risk factor whereas 2.6% had ≥3 risk factors. Men with ≥3 risk factors consumed less vegetable servings compared to those with no risk factor (1.1±0.1 vs 1.4±0.1, p<0.001). Total FV, and vegetable intake were low in women with ≥3 risk factors than in those with none (total FV: 1.4±0.3 vs 2.2±0.3, p=0.003; vegetables: 1.1±0.1 vs 1.4±0.1, p=0.005). Regarding individual risk factors, higher total FV intake, and only fruit intake were unusually associated with higher odds of low HDL cholesterol in men (total FV: Q1->Q4, p for trend=0.025; fruits: Q1->Q4, p for trend=0.03). Increasing intake of total FV was inversely associated with abdominal obesity in women (Q1->Q4, p for trend=0.04). In addition, fruit, but not vegetable intake, non-significantly reduced the odds of abdominal obesity (p for trend=0.07) and high blood pressure (p for trend=0.06) in women. Conclusion We found low consumption of vegetables in both genders, and low consumption of total fruits and vegetables in women with ≥3 risk factors. In addition, total fruits and vegetable intake was inversely associated with abdominal obesity in women. However, the controversial finding that a high risk of low HDL cholesterol is linked to higher FV or fruit intake in men deserves further research. Results suggest a favorable role of fruits and vegetable intake in metabolic syndrome risk factors in this population.