Early fetal and placental MSCs have translationally-advantageous characteristics compared to later pregnancy MSCs. During the first trimester, the fetus and placenta grow rapidly with divergent developmental requirements, but studies comparing mesenchymal stem cells (MSCs) from different origins have paid little attention to the effect of gestational age over this temporal window. Here we present the transcriptome through first trimester development of MSC isolated from fetal bone marrow (BM) or placental structures. Samples were collected weekly from 8 to 12 weeks. The raw microarray data are available on the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-TABM-1224. Additionally, the data have been integrated into the stem cell collaboration platform www.Stemformatics.org. These data provide a valuable resource for developmental biology and stem cell investigation.