We examined the relationship between dietary folate intake and periconceptional use of folic acid (FA) supplements, and small-for-gestational age for weight (SGA-W) and height (SGA-H). The study is based on 786 Spanish women aged 16 years or above, who attended the first-term prenatal population-based screening programme (10–13 weeks) at the reference hospital ‘La Fe’, Valencia, with singleton pregnancy. Periconceptional use of FA supplements was categorised as non-users, moderate users ( ≤ 1 mg/d) and high users (>1 mg/d). Babies born to mothers who used high doses of FA supplements had a significant reduction in mean birth height compared with babies of non-users (β = − 0·53, 95 % CI − 0·96, − 0·09). As regards weight, mothers using moderate and high doses of FA supplements had lower-birth-weight babies for gestational age than non-users (β = − 22·96, 95 % CI − 101·14, 55·23; β = − 89·72, 95 % CI − 188·64, 9·21, respectively), although these decreases were not significant. Results from the multivariate logistic regression models showed that high FA supplement users had a higher significant risk for SGA-H (OR 5·33, 95 % CI 2·08, 13·7), and that users of moderate doses were not associated with a higher risk of either a SGA-W or a SGA-H baby. In contrast, increased quintiles of the dietary intake of folate were associated with a decreased risk of SGA-W (P for trend = 0·002), although no association was observed for SGA-H. Our findings suggest that periconceptional use of FA supplements greater than 1 mg/d is associated with decreased birth height and may entail a risk of decreased birth weight.