Asynchrony of trophectoderm elongation, gestational days 11-12, is evident in porcine concepti, and rapid progression through this phase has been associated with conceptus competency. The goal of the current study was to determine the extent of transcriptomic responses of concepti to developmental delay and their physiological implications. Gestational day 11 concepti with the same morphology, ovoid and 7-8 mm, were isolated and designated as control or developmentally delayed if collected from a homogenous ovoid conceptus population or heterogeneous conceptus population (ovoid to filamentous), respectively. Total RNA prepared from four distinct control and four distinct developmentally delayed concepti, was analyzed using an Agilent high-density custom porcine microarray. Two hundred nine transcripts were found differentially expressed between normal and developmentally delayed concepti. Functional analysis of these genes indicated that a significant number of the genes regulate signal transduction/transcription, organismal development, metabolism, and cell adhesion and can be modulated by transforming growth factor β1 (TGFβ1). Ten genes were selected for real-time PCR validation of differential expression based on a known role in steroid synthesis, endometrium receptivity, and modulation of trophoblast differentiation/growth or interaction with TGFβ1. As in the microarray, all except one, achaete-scute complex homolog 2, were preferentially up-regulated in delayed concepti. Overall, findings suggested that despite similar morphology, the transcriptome of developmentally delayed concepti is distinct from control counterparts. Also highlighted were ways by which the conceptus' microenvironment might be affected and developmental factors that may be of interest to interrogate further to determine if, and how, they affect embryo competency/elongation.