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Cleaning and disinfection (C&D) of poultry houses is an essential aspect in farm hygiene management. Adequate performance of the different steps of a C&D protocol and the use of suitable products are key to prevent and control zoonoses and animal diseases. Hygiene monitoring on total aerobic flora through sampling with agar contact plates at different locations of the poultry house results in a hygienogram score that is used to evaluate the proper execution of C&D.This study analyzed the hygienogram scores of 19,739 poultry flocks in Flanders after C&D. Data relating to the C&D protocol, i.e., year, season, husbandry system, production type, cleaning product, sampler, active components of the disinfectant, disinfection time, disinfection temperature, and disinfection responsible, were collected.The average hygienogram score decreased significantly over time, suggesting a general improvement between 2007 and 2014. Differences in scores were found among the husbandry systems, with the barn/aviary system having a significantly better hygienogram score compared to the floor house, furnished cage, and battery. Significantly better scores also were found when a cleaning product was used in the C&D protocol. Disinfection with a peracetic acid and hydrogen peroxide combination or formaldehyde gave the best scores. In addition, C&D protocols using ≥2 different disinfectants showed improved results compared to the use of one single disinfectant. Finally, disinfection applied by a specialist contractor resulted in a better score compared to disinfection by the farmer.In conclusion, analysis of the hygienogram scores and related data allowed identifying several factors, resulting in an improvement, which may reduce the total bacterial load in poultry stables and, consequently, the number of zoonotic and pathogenic micro-organisms.