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Objective: To investigate the consequences of removing embryos from the incubator daily, and exposing them to ambient air at 37.0 °C for short periods of time, on embryo development, gene expression and the health of the conceptus. Methods: An in vitro cross-sectional study was undertaken using CBA F1 mouse zygotes exposed to ambient air at 37.0 °C for 3, 5, and 8 min daily during their entire in vitro development. Blastocysts were analyzed for total cell numbers, apoptosis, and H19 and Igf2 expression and transferred to pseudopregnant recipient females to examine pregnancy, fetal and placental weight, and placental H19 and Igf2 expression. Results: Short exposure of pre-implantation embryos to ambient air at 37.0 °C resulted in a statistically significant reduction in blastocyst development and total cell numbers, increased apoptotic cell index, and impaired H19 and Igf2 expression in the blastocyst. Implantation rates were significantly reduced and fetuses and placentae displayed a significant reduced weight on day 18 of pregnancy. Placentae displayed significantly reduced levels of H19 and Igf2 expression. Conclusions: Exposing mouse pre-implantation embryos to ambient air at 37.0 °C, even for brief periods for routine micromanipulations is detrimental to normal embryonic development. Our results highlight the importance of how small alterations in the culture environment can have major consequences for the health of the embryo.