Over 50% of women experience musculoskeletal pain in the low back or lower extremity during pregnancy. Further, 31% of these women experience continued pain after giving birth. Many women also report changes in foot length and arch height during pregnancy. The purpose of this study was to determine if changes in foot anthropometry during pregnancy are related to low back and lower extremity pain. A secondary aim was to determine if added weight alone explains changes in lower extremity alignment, or if other factors mediate these changes. Methods:​ Fifteen primigravid women were recruited to participate, along with thirteen weight-matched nulliparous controls. Several measures of foot and lower extremity alignment were assessed during the 1st, 2nd, and 3rd trimesters, as well as post-partum. These measures included:​ foot length, foot width, arch index, arch height index, arch rigidity index, arch drop, rearfoot angle and pelvic obliquity. Musculoskeletal pain was assessed using a Visual Analogue Scale. Controls and participants who had not yet reached the full weight of pregnancy repeated measurements weighted with a pack worn over the anterior trunk. Results:​ Over the course of a first pregnancy, significant changes were seen in foot length, arch index and pelvic obliquity. Added weight alone produced significant changes in arch drop and arch rigidity index only. Changes in foot width, standing arch height index and pelvic obliquity were related to pain at the low back, hip and knee during pregnancy. Conclusion:​ Pregnant women experience changes in lower extremity anthropometry and alignment that may contribute to musculoskeletal pain.