In a parallel study, alterations to gestational nutrition increased indicators of fertility in female offspring. The aim of this study, using the same cohort of animals, was to apply RNAseq to fetal ovaries to identify potential genes and pathways which may underlie the relationship between gestational nutrition and post-natal fertility. cDNA libraries were constructed and sequenced using Ion Proton from 5-6 fetal ovaries at both days 55 and 75 of gestation. Pregnant ewes were exposed to either a maintenance diet or 0.6 of maintenance for the first 55 days of gestation followed by an ad libitum diet. Of approximately 16,000 sequences 65 were differentially expressed at day 55 and 145 differentially expressed at day 75. At both gestational ages genes expressed preferentially in germ cells were common. Enriched Gene ontology terms included ion transport, nucleic acid binding, protease inhibitor activity and carrier proteins of the albumin family. Affected pathways identified by IPA analysis included LXR/RXR activation, FXR/RXR activation, pathways associated with nitric oxide production and citrullination (by NOS1), vitamin c transport and metabolism, and REDOX reactions. The data offers some insights into potential mechanisms underlying the relationship between gestational nutrition and post-natal fertility seen in these animals. Particularly the roles of nitric oxide and protease inhibitors in germ cell development are highlighted and warrant further study.