For many years, ultrastructural cytochemistry has been a major tool for investigating the relationships between the structure and the functions of the cell nucleus. This article shortly reviews the contributions of transmission electron microscopy to the in situ studies of intranuclear distribution of chromatin domains and of essential nuclear functions, such as DNA replication, transcription and pre-mRNA processing. It attempts to analyse the role of different nuclear structural domains in nuclear functions, as well as further directions in this important field of research.