Objectives Babies born small for gestational age (SGA) have a higher risk of neonatal morbidity and mortality as well as later life chronic disease. The objectives of this study were to examine the extent to which prepregnancy body mass index (BMI) and gestational weight gain (GWG) influenced risk of SGA among Japanese, and to evaluate physician response to, and potential effects on, GWG. Methods We examined SGA risk as a function of maternal BMI and GWG using logistic regression with data from maternal child health handbooks obtained from women in Japan (N = 383). Physicians’ written comments on weight and dietary restriction were analyzed for responses to and influence on GWG. Results SGA babies comprised 8.6% of the sample, with 13% and 6% of the mothers being underweight and overweight, respectively, and 21.7% and 19.8% of mothers gaining less and more than the recommended amounts, respectively. In adjusted models, higher prepregnancy BMI and GWG were associated with lower risk of SGA (OR 0.71, 95% CI 0.56, 0.90; 0.75, 95% CI 0.61, 0.92 respectively) in models for girls, but not for boys. Inadequate GWG was associated with higher risk of SGA in girls (OR 6.64, 95% CI 2.18, 20.22). Physician written instructions to restrict dietary intake and weight gain followed an average weight gain of 0.69 kg/week from the previous prenatal exam, and were followed by weight gains that decreased to 0.30 kg/week. Conclusions Prepregnancy BMI and GWG significantly influence SGA risk in female babies. GWG may be influenced by physicians’ recommendations. Am. J. Hum. Biol. 28:714–720, 2016. © 2016 Wiley Periodicals, Inc.