This study is part of the BioMadrid Project, a bio-monitoring study designed to assess pollutants in the environment surrounding children born in the Madrid region. Our aim in this report is to evaluate the association between prenatal lead exposure and fetal development using three biological samples (maternal and paternal blood lead at around 34 weeks of gestation as well as cord blood lead levels), three biomarkers of effect in cord blood peripheral lymphocytes (micronucleus in binucleated cells, nucleoplasmic bridges, and nuclear buds), and different anthropometrical characteristics at birth. Maternal and cord blood lead were not associated with newborn measurements or genotoxicity biomarkers. In contrast, increases in father blood lead were coupled with lower weight (mean difference (MD), -110.8 g; 95 % confidence intervals (95%CI), -235.6 to 6.00; p < 0.10) and shorter abdominal (MD, -0.81 cm; 95%CI, -1.64 to 0.00; p < 0.05) and cephalic (MD, -0.32 cm; 95%CI, -0.65 to 0.00; p < 0.05) circumferences at birth as well as with the presence of nucleoplasmic bridges (odds ratio, 1.03; 95%CI, 1.00 to 1.06; p < 0.05) and nuclear buds (odds ratio, 1.02; 95%CI, 0.99 to 1.04; p < 0.10). These associations were mainly confined to female babies, in whom paternal lead was also inversely associated with length. Our results support the hypothesis that paternal lead exposure may be affecting the development of newborns.