Recent advances have rapidly facilitated development of new and improved high-resolution, high-throughput volume electron microscopy techniques. Investigating cell structures and interactions at higher resolution and in three dimensions is becoming increasingly important in parasitology. Understanding the different capabilities of light, X-ray, electron, and ion microscopy technologies is essential for choosing the right technique to solve current and challenging parasitology research questions. Volume electron microscopy techniques are underutilised in most fields of parasitology despite recent improvements in accessibility, user-friendliness, and cost. To best understand parasite, host, and vector morphologies, host–parasite interactions, and to develop new drug and vaccine targets, structural data should, ideally, be obtained and visualised in three dimensions (3D). Recently, there has been a significant uptake of available 3D volume microscopy techniques that allow collection of data across centimetre (cm) to Angstrom (Å) scales by utilising light, X-ray, electron, and ion sources. Here, we present and discuss microscopy tools available for the collection of 3D structural data, focussing on electron microscopy-based techniques. We highlight their strengths and limitations, such that parasitologists can identify techniques best suited to answer their research questions. Additionally, we review the importance of volume microscopy to the advancement of the field of parasitology. [ABSTRACT FROM AUTHOR]