We aimed to validate a method for assessing trans-fatty acid (TFA) intake in the Japanese population using the FFQ developed in the 1990s from a prospective study that was based on the Japan Public Health Center-based Prospective Cohort Study. For FFQ validation, we included 565 participants (Cohort I: n 215, Cohort II: n 350) aged 40–69 years. We used a 28-d dietary record (DR) over 1 year and two FFQ administered before and after DR assessment. We calculated total TFA intake, TFA from industrial oils (i-TFA) and TFA from ruminants (r-TFA) considering a database of measurements obtained mainly from Japan. Spearman’s rank correlation coefficients (CC) were computed for validity and reproducibility. Energy adjustments were applied using two methods considering the TFA measurement: density method for TFA % of total energy and residual method for TFA g/d. The total TFA intake (% of the total energy intake) was 0·08–0·76 % (median, 0·27–0·37 %) in DR of both cohorts and was 0·00–1·13 % (median, 0·30–0·40 %) in FFQ. The i-TFA accounted for approximately 50 % of the total TFA intake in DR and approximately 40 % in FFQ. For total TFA (% of the total energy intake), CC were 0·54–0·69, and weighted κ coefficients were 0·88–0·92 for both cohorts. The de-attenuated CC was 0·46–0·62 for i-TFA (g/d) and 0·57–0·68 for r-TFA (g/d). Our study showed that the validity and reproducibility of TFA intake estimation using the FFQ were reasonable, suggesting its suitability among the Japanese population with low-TFA intake.