Instruments for estimating the intake of food components can be useful in the prevention and/or treatment of diseases related to improper diet. There is, at present, no scientifically validated instrument for estimating consumption of trans fatty acids (TFA) in the Mexican population. The objective of this study was to design and validate such an instrument: a questionnaire that can be used to estimate consumption of TFA from food products. The questionnaire was applied to 162 students from the Autonomous University of Querétaro (UAQ). There were two phases to the study: (1) design of a food frequency questionnaire to assess consumption of trans fatty acids (FFQ-TFA) and an eating practices questionnaire (EPQ-TFA); (2) validation of the instrument. Content validity was measured by expert review and by Aiken’s V method, obtaining an overall score of 0.895. As final tests for the FFQ-TFA analysis, criterion validity was measured using Spearman’s correlation (r = 0.717, p < 0.01) and a linear regression (B = 0.668), considering the results of the 24-h dietary recall (24 HR); and reproducibility or temporal stability was measured using Pearson’s correlation (r = 0.406, p < 0.01). Subsequently, a Pearson correlation was applied between TFA consumption estimated by the FFQ-TFA-2 and the global score from the EPQ-TFA-2 (r = 0.351, p < 0.01). A Pearson correlation was applied between the EPQ-TFA-1 and the EPQ-TFA-2 (r = 0.575, p < 0.01). TFA consumption per day was 2.49 ± 1.32 g in the participating population, which was 1.04 ± 0.51% of their total kcal consumption.