Trypanosomes and Leishmania are two groups of important neglected human pathogens. They are single cell eukaryotes and are active swimmers for many of their life cycle stages. This swimming is vital for the life cycle – inability to swim gives a range of defects, from the dramatic cell death of trypanosomes in the host bloodstream to the inability of Leishmania to transmit through the sandfly vector. A single flagellum drives swimming motility and the flagellum beats at around 40 times per second, demanding camera frame rates upward of 200 frames per second to analyse its movement. Analysing the flagellum by fluorescence microscopy is therefore a significant challenge, but would confer great advantages by allowing the analysis of individual proteins and structures within the cell. We have developed synchronous multi-channel and multi-focal plane widefield fluorescence microscopy capable of visualising endogenously tagged proteins within the flagellum at 200 to 400 frames per second. The ability to visualise multiple channels and multiple focal planes using fluorescence in a live beating flagellum is opens up new opportunities to understand how parasites and other flagellated/ciliated organisms control their motility.