Our objectives were to quantify and characterize potential differences in transcriptome of the corpus luteum (CL) in pregnant (P) and nonpregnant (NP) cows at late diestrus. The estrous cycle of primiparous cows (n = 35) were synchronized using the Presynch-CIDRSynch protocol. On the day of the last GnRH (d 0), 22 cows were selected randomly to be inseminated (AI), while the other cows remained as a nonbred NP group (n = 13). On d 17, all cows were slaughtered and those with an elongating conceptus were classified as P (n = 14). The CL was dissected, weighed, and stored at −80°C. A subsample of CL from P (PCL = 8) and NP (NPCL = 4) cows were subjected to transcriptome analysis using Affymetrix Gene Chip Array. Data were analyzed using Bioconductor software in R. The GCRMA function was used to preprocess the data, and the Limma package was used to fit a linear model and adjust variances by empirical Bayes adjustment. Moderate t-test was performed and P values were adjusted for multiple testing using the BH false discovery rate. Adjusted P < 0.05 and fold change > 1.5 characterized significant differences. A total of 106 transcripts were differently expressed, 67 upregulated and 39 downregulated in PCL compared with NPCL. Differently expressed genes (DEG) were associated with lipid metabolism, small molecule biochemistry, cell-to-cell signaling and interaction, and cell morphology. Among DEG with increased expression in PCL were APLNR (2-fold), HPGD (2-fold), and AKR1C4 (1.8-fold). The first is relevant for angiogenesis, and the latter 2 are related to metabolism and degradation of prostaglandins. Among DEG with reduced expression in PCL were BOLA (4.3-fold), SERPINA14 (1.8-fold), and FAS (1.6-fold). The first is important for antigen presentation and might indicate the abundance of immune cells in the CL, and the latter 2 are important cell survival and tissue remodeling. In conclusion, transcriptome of CL in P and NP cows at late diestrus have important differences that seem to be unrelated to luteolytic signals in NPCL and suggest the presence of endocrine signals derived from the pregnant uterus in the PCL during maternal recognition of pregnancy.