Phthalates are plasticizers finding wide spread use in industrial and household products, with measureable levels of phthalate-derived metabolites in the general US population. Phthalates have endocrine disruption potential and have been implicated as obesogens. Our exploratory investigation to reveal the impact of in utero exposure to a phthalate on the biochemical profiles of the brain, testes, and uterus of prepubertal offspring, and of tissues from dams administered butylbenzyl phthalate (BBP). Pregnant rats (three per group) were administered (on gestation day 14–21) corn oil (control), or 25 mg/kg/day or 750 mg/kg/day BBP in corn oil. Tissues were collected from each of the dams on postnatal day (pnd) 21 (~3 weeks after the end of BBP administration), and from each of the pups on pnd 26 (~4 weeks after birth to dams administered vehicle or BBP during gestation) and processed for metabolomics analysis. Multivariate data analyses revealed metabolites that best distinguished the exposed and control groups. The metabolites most important to distinguishing the study groups were tested for significance using the exact Wilcoxon rank-sum test. Male pups had significant differences (control versus BBP dose groups) in levels of metabolites for both the brain and testes even at the P < 0.01 level. However, female pups and dams had significant testing for the uterus only at the P = 0.1 level tested. Female pups also had some significant differences for the brain with P values between 0.5 and 0.1. Amino acid metabolism (male and female pups) and phospholipid metabolism (male pups) were perturbed for the brain. Amino acid metabolism, purine metabolism, and TCA cycle were perturbed for tests and uterus. This study demonstrated the use of metabolomics to reveal metabolic perturbations in tissues of offspring following in utero exposures, and suggests the use of this approach for determining the impact of exposure past the time of the presence of the parent compound and metabolites derived from the parent compound.