Background Natural disasters increase the level population stress, including pregnant women, who can experience prenatal maternal stress, affecting the fetus and triggering perinatal complications, such as low birth weight, smaller head circumference, etc. However, little is known about effects of earthquake on perinatal outcomes. Objective To evaluate the effect of earthquake occurred on February 27, 2010 and perinatal outcomes of Chilean pregnant women, and to examine these effects by timing of exposure during pregnancy and newborn gender. Methods A register-based study was performed using data collected from women who had a vaginal delivery in a large private health center in Santiago, Chile, during 2009 and 2010. The study population was categorized according to exposure to earthquake and timing during gestation. Primary perinatal outcomes were gestational age at birth, birth weight, length and head circumference. Analyses adjusted for gender, gestational age at exposure, parity, maternal age and income. Results A total of 1,966 eligible vaginal deliveries occurred during 2009 and 2,110 in 2010. Birth weight was not affected by the trimester of exposure; however, length, head circumference and gestational age at birth were significantly different according to trimester of exposure and gender of newborn. In multivariable analysis, newborns were shorter by 2 mm, 5 mm and 4.5 mm, if they were exposed during their first, second and third trimester, respectively. Furthermore, newborns had a smaller head circumference by 1.2 mm and 1.5 mm if they were exposed during first and second trimester of gestation. Conclusion In this cohort, exposure to the February 2010 earthquake resulted in earlier delivery and reduced length and head circumference in the offspring. This association varied according to trimester of exposure and fetal gender. Health workers should include exposed to high levels of stress associated with natural disasters when assessing pregnancy risk factors.