Histomonas meleagridis was held primarily responsible for an outbreak of 6% increased mortality and 11% decreased egg production between weeks 57 and 72 in a flock of free-range layer hens, concurrently infected with Brachyspira-like bacteria. This case can be considered an example of ancient diseases re-emerging in alternative housing systems that are promoted because of animal welfare considerations, but that at the same time allow rapid spread of pathogens in birds for which only few curative drugs are registered. Therefore, new housing methods should be introduced gradually to gain experience with them.