Decidualization involves the differentiation of the endometrial tissue into the decidual tissue of the pregnant uterus in several species including humans and rodents. This differentiation occurs only after the onset of implantation in mice and can be artificially-induced causing the formation of deciduomal tissue. The purpose of this study was to identify a group of differentially expressed genes between the developing decidua and deciduoma and study their expression as it may relate to conceptus influenced changes in endometrial gene expression during decidualization. In this study we artificially induced decidualization by transferring blastocyst-sized ConA-coated agarose beads into the uterus on Day 2.5 of pregnancy as we had previously found this model to be more "physiological". Total RNA was isolated from implantation sites of the uteri of pregnant mice as well as pseudopregnant mice that received beads. This RNA was then used for microarray analysis using Mouse Illumina Beadarray chips. This revealed potential differential mRNA levels of over 1,000 genes between the decidua and bead-induced deciduoma tissues of Day 7.5 pregnant and pseudopregnant mice, respectively. Of these, the mRNA levels of 102 genes were 2-fold greater in the decidual tissue while almost twice as many were 2-fold greater in the deciduoma. The broad functions of the protein encoded by the mRNAs included protein binding (e.g. Copz1, Gjb2, Dctn1, Islr, Nisch, Wwc1, Cdc20, Rxrb, Klhl7, Adam10), calcium transport (e.g. Anxa6, Itga11, Clta, Smoc2, Vdr), hydrolase/peptidase activity (e.g. Klk5, Klk26, Klk24, Tmprss4, Ptpn14, Ddx3x, Atp1a2, Usp25, Smarca1), ligase activity (e.g. Iars, Farsla, Ube2v1, Cbll1, Rnf19, Mccc1), and transcription (e.g. Irf1, Hip1, Bhlha15, Supt6h, Scand1, Myocd, Sp3, Mitf, Papolg). We confirmed the differential mRNA levels of a number of gene transcripts using quantitative RT-PCR. Finally, the level and localization of some of the mRNA's identified by our microaray analysis were examined in the mouse uterus during decidualization in more detail and included: Aldh3a1, Bcmo1, Guca2b, GCC, and Inhbb. Localization of mRNA expression in the Day 7.5 implantation site occurred in the mesometrial region near the lumen (Aldh3a1), luminal and glandular epithelia (Guca2b), and endothelial cells lining the sinusoids (Inhbb). This study provides the identity and expression analysis of steady-state mRNA levels of genes whose expression may be influenced by the conceptus using a physiological model for implantation.