FFQ comprising food items, intake frequency categories and portion sizes have been used in large-scale observational studies to assess long-term dietary exposure. Although gender is an important influence on food choice and portion size, gender differences are not often analysed during FFQ development. This study investigated whether gender differences were considered sufficiently when developing FFQ, which affects the results of validation studies. A PubMed search using combinations of ‘FFQ’, ‘Food Frequency Questionnaire’, ‘Validation’ and ‘Validity’ identified 246 validation studies available in English, published between January 1983 and May 2014, which included healthy male and female adults. The development process of the 196 FFQ used in the 246 validation studies was examined. Of these, twenty-one FFQ (10·7 %) considered gender during item selection or portion size determination, and were therefore classified as gender specific (GS), but 175 (89·3 %) did not consider gender, and were classified as ‘not gender specific (NGS)’. When the ratios between intake levels obtained using the FFQ and a reference method for energy and seven nutrients were compared between the GS group and the NGS group, more significant differences were observed in women than in men (four v. one nutrient). Intake of three nutrients was significantly underestimated in both sexes in the GS group. In the NGS group, nutrient intakes were significantly overestimated more often in women than in men (four v. one). These results indicate that not considering gender in FFQ development causes greater inaccuracy in dietary intake assessment in women than in men. Results of nutritional epidemiological studies should be re-evaluated for their validity, especially if the studies used NGS-FFQ.