Lycopodium clavatum marker-grain tablets are often added before palynological processing to calculate the absolute abundance of organic-walled microfossils in sediments. In this study we investigate the reproducibility of dinoflagellate cyst concentrations by performing nine different tests: varying dinoflagellate cyst/Lycopodium spore ratios, sample weights, centrifuge speeds and times, sonication times, and mesh sizes; manually powdering the sediment using a mortar and pestle prior to processing, using a water jug instead of squirt bottles during sieving, decanting over a 6 μm sieve and adding Lycopodium tablets at the end. Previous studies have reported loss of Lycopodium spores during processing. In this study we investigate sources of this loss by microscopically analyzing residue on stir sticks and sieves, and what is lost through the sieves and decanting. We document an average loss of 8.2 % of Lycopodium spores during processing, with the greatest loss occurring through the fine sieve and resulting in only a 4.8% overestimation of the cyst concentration. Results using powdered sediment and sonicating for more than 5 min are less reproducible. Large cyst/Lycopodium spore ratios were found to have higher cyst concentrations and standard deviations, thus we recommend ratios of less than five, and ideally ratios between 0.5 and 2 to facilitate counting.