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Abstract Background Research published to date on the relationship between insulin resistance (IR) and fructose consumption is scarce, has used different methods, and has yielded sometimes contradictory results. This study aims to determine whether a low-fructose and/or low-sucrose diet supervised by a physician or nurse decreases IR compared to a standard diet. Methods/design This field trial is located at primary care centers. The participants are adults aged 29 to 66 years, with a Body mass Index (BMI) between 29 and 40.99 kg/m2 and without diabetes. To date, 245 participants have been assigned randomly to the low-fructose diet intervention group (LFDI) at health centers in the western health service zone of Tenerife island, and 245 to the standard-diet control group (SDC) at health centers in the eastern health service zone. Recruitment is opportunistic and is carried out by physicians and nurses at participating health centers. Initially (baseline), and after 24 weeks of intervention, dietary records, physical activity, waist circumference, BMI, blood pressure, fasting blood glucose and insulin concentrations (HOMA2-IR) and lipid profile are recorded; blood glucose and insulin and lipid profile are also recorded 2 h after a 75-g glucose overload. After 48 weeks (24 weeks after the intervention), fasting blood samples are again obtained and a physical examination is performed. All tests and measures are repeated and recorded except dietary records, physical activity and oral glucose overload. Low-fructose diets are designed by calculating free and total (free + fructose associated with sucrose) fructose contents in standard diets, and removing foods with a fructose content in the highest quartile for the amounts in the standard diet. Participants in both groups are prescribed a diet that contains 30 to 40% less than the participant’s energy requirements. The primary endpoint is change in HOMA2-IR between baseline and week 24, and other outcomes are change in HDL-cholesterol, LDL-cholesterol, triglycerides , waist circumference to height ratio and BMI. The secondary endpoint is change in HOMA2-IR between week 24 and week 48 together with the outcomes noted above. Comparisons between groups for variables used to indicate IR levels are done with a Student’s t test for unpaired variables or the Mann-Whitney U test if the distribution is not normal. Multivariate regression models will be used to control for confounding factors not accounted for in the study design, and for independent prognostic factors. Discussion If the dietary intervention being tested, i.e., a diet low in fructose/sucrose, is able to reduce IR, the results – if translated into regular clinical practice – could provide a hitherto unavailable tool to prevent type-2 diabetes mellitus. Trial registration ISRCTN, ID: ISRCTN41579277 . Registered retrospectively on 15 November 2016.