Introduction: This study aimed to investigate whether a rich flaxseed diet could modify the micronuclei frequency, nuclear anomalies and biochemical and anthropometric parameters in metabolic syndrome patients. Material and methods: Fifty-eight patients with metabolic syndrome were dichotomized into two groups, namely, the control group (CG) and the intervention group (IG), and the patients in the IG received a diet supplemented with flaxseed. The anthropometric and clinical parameters were measured. Nuclear anomalies isolated from the oral mucosa were analyzed at the beginning and end of the 3-month follow-up. Results: After the nutritional follow-up, the percentage of fat was decreased in the CG (before, 45.40%; after, 37.89%, p < 0.001). In the IG, the weight (before, 81.03 ±13.17 kg; after, 79.81 ±13.47 kg, p = 0.01), body mass index (before, 32.7 ±5.4; after, 32.2 ±5.6, p = 0.009) and very-low-density lipoprotein (before, 31.96 ±15.23; after, 26.13 ±7.54, p = 0.04) were decreased. The frequencies of MN (micronucleated) and BN (binucleated) cells were decreased in the CG (before, 14.03 ±5.28, after 11.17 ±3.68; before, 2.66 ±3.5, after, 1.10 ±1.66; p = 0.001/0.02, respectively), while in the IG, the frequencies of MN and BN cells and NB (nuclear buds) were decreased (MN before, 4.97 ±5.