Adverse conditions in utero can have transgenerational effects, in the absence of a subsequent insult. We aimed to investigate the contribution of the maternal pregnancy environment vs. germ-line effects in mediating alterations to cardio-renal and metabolic physiology in offspring from mothers born small. Uteroplacental insufficiency was induced by bilateral uterine artery and vein ligation (Restricted) or sham surgery (Control) in Wistar-Kyoto rats. Restricted and Control female offspring (F1) were mated with either breeder males (embryo donor) or vasectomised males (embryo recipient). Embryo transfer was performed at embryonic day (E) 1 whereby second generation (F2) embryos gestated (donor-in-recipient) in either a Control (Cont-in-Cont, Rest-in-Cont) or Restricted (Cont-in-Rest, Rest-in-Rest) mother. In male and female offspring, glomerular number and size were measured at postnatal day (PN) 35 and systolic blood pressure, glucose control, insulin sensitivity and pancreatic β-cell mass were measured in separate sibling cohorts at 6 months. Rest-in-Rest offspring were hypothesised to have similar characteristics (reduced growth, altered metabolic control and hypertension) to non embryo-transferred Rest, such that embryo transfer would not be a confounding experimental influence. However, embryo-transferred Rest-in-Rest offspring underwent accelerated growth during the peri-pubertal phase, followed by slowed growth between 2-3 months of age compared with non embryo-transferred Rest groups. Furthermore, renal function and insulin response to a glucose load were different to respective non embryo-transferred groups. Our data demonstrate the long-term effects of in vitro embryo manipulation, which confounded the utility of this approach in delineating between the maternal pregnancy environment and germ-line effects that drive transgenerational outcomes.