In European eel, it has been proposed that the undifferentiated gonad would develop into either an intersexual stage (Syrski organ) or directly into an ovary. The Syrski organ could then develop into either an ovary or a testis. In the present study, glass eels were raised until they reached a minimum size of 29 cm for histological sex assessment. In addition, some undifferentiated individuals with size encompassing 15–28 cm were sampled in a female-biased population (Oir River). We also investigated aromatase gene expression, which is known to be involved in the process of fish sex differentiation. Gonad histology revealed that intersexual eels were characterized by a small number of oocytes within a predominant testis-like structure. Males were significantly smaller than intersexual eels, which suggests that all males do not necessarily pass through an intermediate intersexual stage. Aromatase transcript levels in intersexual eels gonads and testes were similar but significantly lower than in ovaries and were comparable between ovaries and undifferentiated gonads from the females-biased population. In addition, condition factor was lower in female than in intersexual individuals. Together, these results provide evidence that ovaries would not develop from the Syrski organ.