Due to consumers demand, alternative housing systems are rapidly expanding in Quebec and Canada. Egg farmers may choose to invest in enriched colony housing system or aviaries, but with the trend for free roaming hens, some ‘old’ diseases are re-emerging. Coccidiosis, caused by protozoan Eimeria species, has an impact on intestinal integrity, and might allow for the development of necrotic enteritis. Nematodes, including Capillariidae, and Ascarididae, can also affect the health of laying hens as well as egg quality, while red mites (Dermanyssus gallinae), can cause serious production losses. Our hypothesis is that the incidence of pathogens and associated diseases is higher in aviaries than in enriched colony housing systems. Objectives were to compare Eimeria excretion curves and the incidence of the intestinal and external parasites between the two egg laying housing systems between 19 to 65 weeks of age.