Axonemes form the core of eukaryotic flagella and cilia, performing tasks ranging from transporting fluid in developing embryos to the propulsion of sperm. Despite their abundance across the eukaryotic domain, the mechanisms that regulate the beating action of axonemes remain unknown. The flagellar waveforms are 3D in general, but current understanding of how axoneme components interact stems from 2D data; comprehensive measurements of flagellar shape are beyond conventional microscopy. Moreover, current flagellar model systems (e.g., sea urchin, human sperm) contain accessory structures that impose mechanical constraints on movement, obscuring the "native" axoneme behavior. We address both problems by developing a high-speed holographic imaging scheme and applying it to the (male) microgametes of malaria (Plasmodium) parasites. These isolated flagella are a unique, mathematically tractable model system for the physics of microswimmers. We reveal the 3D flagellar waveforms of these microorganisms and map the differential shear between microtubules in their axonemes. Furthermore, we overturn claims that chirality in the structure of the axoneme governs the beat pattern [Hirokawa N, et al. (2009) Ann Rev Fluid Mech 41:53-72], because microgametes display a left-or right-handed character on alternate beats. This breaks the link between structural chirality in the axoneme and larger scale symmetry breaking (e.g., in developing embryos), leading us to conclude that accessory structures play a critical role in shaping the flagellar beat.digital holographic microscopy | low Reynolds number | ciliary and flagellar motion | malaria transmission F lagella and cilia are ubiquitous across the eukaryotic domain.They perform critical roles such as the propulsion of microorganisms and sperm, sensory detection, and transport of fluids in the brain (1-3). Although the appearance of motile cilia and flagella can vary in different organisms, it is based on an underlying structural motif: a cylinder of nine microtubule doublets that move lengthwise relative to each other under the action of dynein molecules. The peripheral doublets in the axoneme often surround a central pair of singlet microtubules; the whole structure is then referred to as a "9+2" axoneme. Interestingly, motility does not seem to be contingent on the central microtubules. Motile flagella with three, one, or zero central microtubules (4, 5) have been reported. Dynein molecules are distributed along the length of each of the peripheral doublets asymmetrically. Viewed from the axoneme's basal end, the dyneins are permanently anchored to one doublet and face its clockwise neighbor, where they can attach and move longitudinally. This structural chirality has been invoked as the underlying cause of symmetry breaking in developing embryos (6). Certain "nodal" cilia present in the early stages of development have been shown to rotate consistently in the same direction, counterclockwise, viewed from the basal end. The collective effect from many such cilia is unidirectio...