Aim Betaine can promote methylation as a methyl donor and play an important role in the regulation of lipid metabolism, and may affect infant birth weight. The aim of this study is to assess whether betaine is associated with poor fetal growth. Methods A total of 141 mother–infant pairs were enrolled in the study. According to gestational age and birth weight, the mother–infant pairs were divided into small-for-gestational-age and appropriate-for-gestational-age group. Cord plasma concentrations of betaine and lipid (triglyceride, low density lipoprotein, high density lipoprotein and total cholesterol) were measured. Results Cord plasma betaine concentrations were higher in small-for-gestational-age (4.37 ± 0.98l ng/ml, P = 0.016) relative to appropriate-for-gestational-age (3.98 ± 0.86 ng/ml) newborns, and were not correlated to lipid levels (all P > 0.2). Adjusting for maternal and neonatal characteristics, birth weight (β = -70.32, p = 0.016) and birth length (β = -0.298, p = 0.029) were negatively correlated with the levels of betaine. Higher betaine concentrations were associated with increased risks of small-for-gestational-age (OR = 1.798, P = 0.008). Conclusions This study demonstrate that elevated concentration of betaine in cord blood is associated with higher risk of small-for-gestational-age and this association is independent of lipid levels. The dysregulation of betaine in infants may be a risk factor for fetal growth.