Primordial follicles are the sole resource for oocytes in mammals, but in vitro ovarian culture systems provide an opportunity to expand upon gametogenesis. Previous work has shown that mouse foetal gonads cultured with media containing oestrogen produce abnormal follicles. However, high levels of oestrogen are found in the in vivo environment. Now, Yayoi Obata and colleagues suggest how mouse follicle formation occurs with endogenous oestrogen in vivo. The authors show that pharmalogically blocking oestrogen receptors (primarily ESR1) prevents oocyte abnormalities in culture. Comparing gene expression between cultured and P0 mouse ovaries, they reveal that anti-Mullerian hormone (Amh) is overexpressed in culture, which is reduced when oestrogen signalling is blocked. Furthermore, chromatin immunoprecipitation (ChIP) qPCR shows that ESR1 directly drives ectopic expression of Amh, and addition of AMH to the culture media causes abnormal follicle formation. Finally, the addition of alpha-fetoprotein (AFP), which is produced in the foetal liver in vivo, to the culture media reduces oestrogen-dependent Amh expression and improves follicle assembly. These data indicate that, in culture, media-derived oestrogen acts through ESR1 to drive Amh expression, causing follicle abnormalities. In vivo, AFP potentially blocks endogenous oestrogen. This work provides new approaches to improve ovarian culture systems.