Doctoral education is a key feature of university systems, as well as a basic foundation of scientific practice. That period culminates in a dissertation and examination of the candidate that has been studied from several points of view. This paper reports the results of an analysis on the evolution and characteristics of gender imbalance of a complete doctoral system for a wide period of time. Data from the database Teseo was used in order to identify the individuals involved in the process, the scientific fields in which the dissertations where classified, and the institutions in which the examination took place. Results: the Spanish system shows a clear evolution towards gender balance, but also some concerning trends that are worth tracking. Seemingly, STEM disciplines look to be evolving more slowly than other branches of science in several aspects. A leaky pipeline is characterized in this system around the roles of supervisors, candidates, members and chairs of the dissertation committees. Gender assortativity is also studied and described, and its possible effects discussed around the academic relations that surround doctoral examination.