The majority of pregnancy loss in cattle occurs between days 8 and 16 of gestation coincident with the initiation of conceptus elongation and the onset of maternal recognition of pregnancy. Conceptus elongation is associated with an increase in interferon-tau synthesis and is driven by conceptus-endometrial interactions. The objective of this experiment was to characterize differential patterns of mRNA expression between short and long bovine conceptuses recovered on Day 15 of gestation. Embryos were produced from superovulated Holstein donor cows and Grade 1 compact morulas were transferred in groups into recipient heifers at Day 6.5 of the cycle with each transfer group consisting of 3 to 5 embryos. Conceptuses were then recovered at Day 15 of gestation, measured to assess overall length, and examined to verify the presence of an embryonic disc. Total RNA was extracted from complete, intact conceptuses classified as either short (mean ± SEM length of 4.29 ± 0.15mm; range of 4.0-4.7mm, n=5) or long (mean ± SEM length of 24.67 ± 1.91mm; range of 18.9-29.8mm, n=5) and analyzed on individual GeneChip Bovine Genome Arrays (Affymetrix, Inc.). Statistical analysis was performed using JMP Genomics (SAS, Inc.) and pathway analysis was performed using MetaCore (GeneGo, Inc.). A total of 1,333 genes were differentially expressed (P<0.05) between long and short conceptuses. Of these, 632 genes were up-regulated (P<0.05) and 701 were down-regulated (P<0.05) in long conceptuses compared to short conceptuses. At a significance level of P<0.02, a total of 273 transcripts were differentially expressed between long and short conceptuses. Of these, 147 were up-regulated (P<0.02) and 126 were down-regulated (P<0.02) in long conceptuses compared to short conceptuses. Analysis of known transcripts revealed the most significant cellular pathways affected included ATP, CTP, and GTP metabolism, cholesterol biosynthesis, and classical and alternative complement activation pathways. mRNAs whose expression was significantly (P<0.02) up-regulated in long conceptuses included tumor protein p53 inducible protein 3 (TP53I3), transgelin (TAGLN), proline rich 15 (PRR15), and bone morphogenetic protein 2 (BMP2). In summary, differences in mRNA expression were identified between in vivo produced conceptuses recovered on Day 15 of gestation that were classified based on length. These data can be used to identify mRNAs and cellular pathways involved in enhanced conceptus elongation that may have the potential to serve as markers for pregnancy success. Research supported by NC State University GAANN Biotechnology Fellowship (C.V. Barnwell) and the NC State University College of Veterinary Medicine.