Abstract The establishment of pregnancy is a well-regulated process that involves the development of a viable blastocyst, conceptus elongation, maternal recognition of pregnancy, implantation, and the onset of placentation. Pregnancy loss is a major factor limiting reproductive efficiency in livestock species. In cattle, most embryonic losses occur during the first month of gestation. The genetic and epigenetic regulation of embryonic and placental development in ruminants is still poorly understood. To investigate the transcriptome profile of the bovine conceptus during elongation, Angus heifers (n = 8) were superovulated and bred using semen from a proven high-fertility Bos indicus sire. Heifers were flushed on d 14 of gestation using a standard nonsurgical flushing technique. Recovered conceptuses were individually photographed and snap-frozen for total RNA extraction and bulk mRNA sequencing. Recovered conceptuses were classified based on size into ovoid (0.2 – 5mm; n = 6), tubular (<15 mm; n = 7), or filamentous (>16 mm; n = 7). Differentially expressed genes (DEG: FDR < 0.05) were determined using DESeq2 analysis and were functionally annotated using DAVID. The most pronounced transcriptomic changes were identified between the ovoid and tubular stages, with 5,937 DEGs (2,913 upregulated and 3,024 downregulated) and affected pathways were primarily involved in ribosome assembly and rRNA processing. There were 3,966 DEGs (2,069 upregulated and 1,897 downregulated) between the ovoid and filamentous stages, and the most significant pathways were involved in protein translation, embryonic development, and cell cycle. The transition between tubular to filamentous presented 1,435 DEGs (775 upregulated and 660 downregulated) and significant pathways were involved in protein degradation, cell division, cell cycle, protein stabilization, and mRNA splicing. Our findings indicate that the greatest alterations in the transcriptome occur precisely at the initiation of elongation, suggesting that the bovine conceptus undergoes major structural changes at the outset of this process. This major shift in gene expression is presumed to be necessary to support the subsequent exponential growth phase of elongation, required for maternal recognition of pregnancy.