The reliable collection of peri-implantation embryos in the bovine has important ramifications to post-transfer consequences, particularly in the elucidation of mechanisms associated with post-hatching embryo development and to perturbations in developmental growth following transfer. This study analyzed both in vitro produced (IVP) and somatic cell nuclear transfer (SCNT) embryo-like structures (ELS) recovered at Day (D) 14 and D21. The recovered ELS were subsequently processed for histological examination. At D14 and D21, many of the embryos recovered in the IVP group conformed to the appropriate stage of development. However, a significant number of anomalies were present in the SCNT groups when examined in more detail. Histological examination revealed that irrespective of whether these embryos had undergone trophoblast expansion to an ovoid, tubular or filamentous morphology, many had a degenerated hypoblast layer and a large proportion did not possess an epiblast and therefore could not differentiate into any of the three germ layers as would be expected at the neural groove or somite stage. The prevalence of this developmental pattern was random and did not correlate with treatment (IVP or SCNT) or with types of structures recovered. The rapid embryo elongation period also coincides with the time of greatest embryonic loss and these observations could have important implications for assessing the recovery of embryos post-transfer where incorrect morphological assessment could lead to false implantation and pregnancy determination rates. The implementation of additional methodology is required to adequately characterize the quality of IVP and SCNT-derived embryos collected post-transfer.