Amino acids are critical for the development of the preimplantation mouse embryo to the blastocyst stage. Regulatory roles of amino acids beyond the blastocyst stage, and specifically in pluripotent lineage progression, are not well understood. Here, the expression of SNAT1 (Slc38a1) and SNAT2 (Slc38a2) transporters was determined in mouse embryos between the 2-cell stage and early post-implantation. Both transporters showed dynamic expression patterns. SNAT1 was preferentially expressed on outer cells of the compacted morula that are fated to form trophectoderm (TE). SNAT1 was also detected in all cells of the E3.5 to E5.5 embryo. The preferential expression of SNAT1 in the outer cells of the morula may indicate a requirement for amino acids in TE formation. SNAT2 was detected in the TE, and specifically seen in the nucleus of TE and placenta cells. Nuclear localisation of SNAT2 suggests a novel and as yet uncharacterized role in cell regulation. SNAT2 expression was also detected in the pluripotent lineage, with up regulation of expression in the epiblast prior to primitive ectoderm formation. The pluripotent cells of the early and late epiblast of the blastocyst can be recapitulated in culture with naïve and primed ES cells, respectively. Compared to primed cells, naïve cells showed a reduction in Slc38a2 expression, suggesting that Slc38a2 is regulated at this point of pluripotent cell development. Changes in transporter expression likely reflect different amino acid needs at different stages of development, and the diverse localization of the transporters studied suggests that the role of these proteins extends beyond the supplementation of nutrients from the environment. Understanding the role of amino acids in the development of embryonic cell populations will significantly contribute to the optimisation of media and protocols used in regenerative medicine and assisted reproductive techniques.