The aim of the present study was to compare the hormonal and metabolic characteristics and endometrial gene expression profiles in beef heifers yielding either a viable or degenerate embryo on Day 7 after insemination as a means to explain differences in embryo survival. Oestrus was synchronised in cross-bred beef heifers (n = 145) using a controlled internal drug release (CIDR)–prostaglandin protocol. Heifers (n = 102) detected in standing oestrus (within 24–48 h after CIDR removal) were inseminated 12–18 h after detection of oestrus (Day 0) with frozen–thawed semen from a single ejaculate of a bull with proven fertility. Blood samples were collected from Day 4 to Day 7 after oestrus to measure progesterone (on Days 4, 5 and 7), insulin and insulin-like growth factor (IGF)-I (on Days 4 and 6) and urea (on Day 7) concentrations. All animals were killed on Day 7. Uterine pH was determined at the time of death. Animals from which an embryo was recovered were classified as either having a viable embryo (morula/blastocyst stage; n = 32) or a retarded embryo (arrested at the two- to 16-cell stage; n = 19). In addition, 14 single-celled unfertilised oocytes were recovered, giving an overall recovery rate of 64%. There was no significant difference in the blood parameters determined or uterine pH at the time of death between heifers with either a viable or retarded embryo. The relative abundance of nine transcripts (i.e. MOGAT1, PFKB2, LYZ2, SVS8, UHRF1, PTGES, AGPAT4, DGKA and HGPD) of 53 tested in the endometrial tissue differed between heifers with a viable or retarded embryo. Both LYZ2 and UHRF1 are associated with regulation of the immune system; PFKFB2 is a mediator in glycolysis; MOGAT, AGPAT4 and DGKA belong to the triglyceride synthesis pathway; and PTGES and HGPD belong to the prostaglandin pathway. Both these metabolic pathways are important for early embryonic development. In conclusion, retarded embryo development in the present study was not related to serum progesterone, IGF-I, insulin or urea concentrations, nor to uterine pH at the time of death. However, altered expression of genes involved in the prostaglandin and triglyceride pathways, as well as two genes that are closely associated with the regulation of immunity, in the endometrium may indicate a uterine component in the retardation of embryo development in these beef heifers.