The mechanisms underlying the potential risks of in vitro fertilization and embryo transfer (IVF-ET) have not been fully elucidated. The aim of this study was to explore changes in the complement and coagulation pathways in placentae subjected to IVF-ET in the first trimester compared to placentae from normal pregnancies. Four placenta samples in the first trimester were obtained from patients undergoing IVF-ET owing to oviductal factors only. An additional 4 control placentae were obtained from volunteers with normal pregnancies. A GeneChip Affymetrix HG-U133 Plus 2.0 Array was utilized to analyze the changes in gene expression between the normal and IVF-ET placentae. Differentially expressed genes (DEGs) were analyzed using the Database for Annotation and Visualization and Integrated Discovery bioinformatics resource, and gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted. Using real-time PCR, we confirmed the obtained microarray data in 10 dysregulated genes. Five of the gene products were further analyzed by immunohistochemistry (IHC) to determine their protein expression and localization. A total of fifty DEGs were identified in the complement and coagulation pathways in the IVF-ET treated placentae: 38 upregulated and 12 down-regulated. KEGG pathway analysis indicated that IVF-ET manipulation substantially overactivated the coagulation and complement pathways, while urokinase plasminogen activator-and urokinase plasminogen activator receptor-mediated trophoblastic invasion and tissue remodeling were inhibited. Furthermore, the 5 proteins analyzed by IHC were found to be localized specifically to the placenta. This is the first study to compare DEGs relating to the placental complement and coagulation pathways from patients undergoing IVF-ET treatment compared to those undergoing normal pregnancy. These findings identified valuable biomarkers and potential novel therapeutic targets to combat the unfavorable effects of IVF-ET. Abbreviations: CD59 = CD59 molecule complement regulatory protein, CFD = complement factor D (adipsin), DAVID = Database for Annotation, Visualization and Integrated Discovery, DEG = differentially expressed gene, FGA = fibrinogen alpha chain, FGB = fibrinogen beta chain, FGG = fibrinogen gamma chain, GCOS = gene chip operating software, GEO = Gene Expression Omnibus, GO = gene ontology, IHC = immunohistochemistry, IVF-ET = in vitro fertilization and embryo transfer, PLAU = plasminogen activator urokinase, PLAUR = plasminogen activator urokinase receptor, PROC = protein C, qRT-PCR = quantitative real-time PCR, SERPINC1 = serpin peptidase inhibitor clade C member 1, SERPINE1 = serpin peptidase inhibitor clade E member 1, STRING = search tool for the retrieval of interacting genes, uPA = urokinase plasminogen activator, uPAR = urokinase plasminogen activator receptor.