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Visual evidences undeniably appear more convincing since they can be interpreted easily, though may not be always accurate. The electron microscopy techniques not only allow examining the ultra-structure of various cell/tissue types but also help in proposing the in-depth mechanisms of biological processes. Similarly, comprehensive analysis of the neuronal and synaptic communications, and overall integrity of the brain not only helps us to understand its intricate functioning, but also aids in deciphering the complex human brain disorders. The Drosophila brain and the pair of compound eyes have emerged as favoured organs to investigate the fundamentals of nervous system development and disease biology. Various types of electron microscopy techniques have assisted the Drosophila neurobiologists to generate significant insights about the development, structure and function of different neuronal cell types and their contribution in the aetiology of neurodegenerative disorders. The present review provides a snapshot of the applications of various electron microscopy methods in Drosophila neurobiology research. [ABSTRACT FROM AUTHOR]