Low birthweight has been associated with an increased risk of obesity, insulin resistance, and diabetes in adulthood. The aim of this study was to evaluate IGF-I, adiponectin, insulin levels, and body fat in small-for-gestational-age (SGA) infants at birth. We performed a transverse comparative study in SGA and appropriate-for-gestational-age (AGA) infants. The study was conducted at the Hospital of Gynecology and Obstetrics in Leon, Mexico. Weight, length, and percent of body fat were evaluated during the first 48 h of birth. Glucose, insulin, leptin, adiponectin, and IGF-I levels in cord blood were measured. We studied 100 infants (50 SGA and 50 AGA). A history of diabetes in a second-degree relative was higher in SGA infants than in AGA infants (48.0 vs. 30.0%, respectively; p = 0.03). Glucose, adiponectin, insulin and IGF-I levels were similar between the groups. Leptin levels and percentage of body fat were lower in SGA than AGA (15.3 vs. 23.4 ng/mL; p = 0.003, 11.1 vs. 12.7%; p <0.001, respectively). Logistic regression analysis showed that length, percentage of body fat, and leptin levels were positively associated with birthweight. However, leptin levels were not independent of percentage of body fat. Low body fat and leptin levels, but no evidence of increased metabolic risk at birth, were found in SGA infants.