Protozoan coccidia are one of the most common intestinal parasites in birds. Ordinary coccidian detection and quantification techniques have proved to be inaccurate for wild passerines due to the existence of marked oocyst shedding rhythms throughout the day. Previous studies have suggested that these rhythms should be taken into account when analysing coccidian load and prevalence data, but their pattern and magnitude still remain poorly known. In this study we characterised shedding rhythms in the field by means of 406 samples of faeces taken from two species of passerines with different diets: the European Serin (a granivorous species), and the Garden Warbler (an insectivorous species). Both coccidian prevalence and load were two-phased, with maximums occurring in the afternoon. Oocyst elimination remained consistently high during the second half of the day, whereas prevalence peaked during the afternoon, lowering throughout the evening. This pattern was found in both species. We found a high repeatability of prevalence and intensity when differences between the morning and afternoon were statistically controlled. As a result, we suggest that sampling periods used in the analysis of coccidian prevalence and/or load studies should take into account these differences in times of shedding and be limited to the afternoon, otherwise a statistical control of this factor will be required.