Dietary under-reporting is a common problem when using self-reported dietary assessment tools. However, there are few studies regarding under-reporting during pregnancy. This study aimed to explore the demographic and psychosocial characteristics related to dietary under-reporting in pregnant Japanese women. A cross-sectional study was conducted between 2010 and 2011 at a university hospital in Tokyo, Japan. Nutrient intake was assessed using a self-administered Diet History Questionnaire (DHQ), which had questions about the consumption frequency and portion size of selected food items. The 24-h urinary excretion levels of urea N and K were used as the dietary protein and K intake reference values, respectively. Under-reporting of protein and K was defined as the bottom 25 % of the reporting accuracy (the ratio of reported intake on the DHQ to the estimated intake based on urinary excretion). Under-reporters were defined as participants who under-reported both protein and K intake. Multiple logistic regression analysis was performed to examine the factors associated with under-reporters. Of 271 healthy women at 19–23 weeks of gestation, thirty-five participants (12·9 %) were identified as under-reporters. Under-reporters had a lower pre-pregnancy BMI (adjusted OR (AOR) = 0·81) and lower gestational weight gain (AOR = 0·82); they also reported managing their gestational weight gain with the aim to return to their pre-pregnancy weight soon after childbirth (AOR = 2·99). Healthcare professionals should consider the potential for dietary under-reporting and the possible related factors when assessing the dietary intakes of pregnant Japanese women using self-administered questionnaires.