Pregnancy disorders such as preeclampsia (PE) and gestational diabetes mellitus (GDM) are diagnosed in approximately 5-8% of pregnancies in the United States and substantially higher in under-developed countries. When left untreated PE and GDM greatly increase the risk of neonatal death and long-term disability, as well as maternal death. Post-pregnancy, these diseases have also been linked to an increased risk of cardiovascular and metabolic diseases for the mother. Unfortunately, both PE and GDM screenings are unavailable until 20-28 weeks of pregnancy and are not routinely tested unless the mother meets certain at-risk criteria or specific symptoms. To understand the molecular signatures of each disease and promote earlier diagnosis, plasma samples were acquired from 185 pregnant patients (92 control, 48 PE, 45 GDM) with various phenotypes on the day of delivery. Lipidomic and proteomic analyses were performed on the samples using LC-MS/MS and LC-IMS-MS/MS to elucidate specific molecular changes between mothers with and without these disorders. Proteomic data revealed statistically significant proteins with known functions that varied among diagnoses. Lipidomic data also revealed overall up- and down-regulation of lipid classes specific for GDM and PE patients, as well as variations based on specific fatty acid backbones. When assessed together, the omic analyses illustrated altered mechanisms for each disorder and targets for earlier diagnosis.