Technical Abstract: Gastrulation and trophectoderm elongation of the porcine conceptus coincide with peak conceptus estrogen secretion from gestational day 11 through day 12. The current study aim was to identify genes required for elongation by defining the transcriptome profile of this dynamic tubular stage. The gastrulation and proliferative states of ovoid, tubular, and filamentous conceptuses were also examined. Embryonic disc polarization and growth were examined in the conceptus. An unamplified and two distinct amplified serial analysis of gene expression (SAGE) libraries were generated from tubular conceptus mRNA. Comparing the three libraries at 12,000 tags/library indicated small amplified RNA-SAGE was a more reliable amplification procedure than PCR. The unamplified library was increased to 42,415 tags and statistical analyses of tag frequencies with previously generated ovoid and filamentous libraries revealed the differential expression (p<0.05) of 483 and 364 tags between ovoid:tubular or tubular:filamentous libraries, respectively. Annotation of the tags, identified transcripts involved in development and growth (cytokeratins 8 and 18, stratifin, midkine, and glycolytic enymes), that are potentially regulated by estrogen, and they were analyzed by real-time PCR. The majority of glycolytic enzyme transcripts were constitutively expressed or down-regulated at the filamentous stage. Likewise, cytokeratin mRNAs were decreased in filamentous conceptuses, whereas stratifin and midkine were increased in tubular conceptuses. Analysis of protein revealed distinct expression patterns for cytokeratin 18, stratifin, and midkine. This is the first report of a potential role for stratifin and midkine in porcine conceptus development.