Cross-compliance checks are a tool of the Common Agricultural Policy to promote agri-environmental objectives relating to the environment, animal welfare, and food safety. This mechanism consists of paying direct subsidies to farmers who comply with prescribed requirements. Compliance with animal welfare requirements in the Czech Republic is supervised by the State Veterinary Administration. This study aimed to find the main deficiencies identified as part of cross-compliance checks and to assess the trends of the most frequent defects during the period under review, i.e. 2016–2020. The data for the analysis were received from the Central Veterinary Administration of the State Veterinary Administration and included the results of 2,031 checks carried out. Shortcomings were found in 14.52% of cases. Detailed analysis showed that significantly (P < 0.05) the highest frequency of violations was found in the areas of ‘nutrition and watering’ (294; 29.85%) and ‘spatial requirements’ (274; 27.82%). Based on the evaluation of trends, a significant (P < 0.05) decrease in the frequency of violations in the field of compliance with holder duties and animal hygiene standards of animals was detected. The results of this work show that animal welfare is continuously improving on farms. However, the aim should be to reduce deficiencies to a minimum for all indicators. In view of the results of this study, it is necessary to focus primarily on improving the quality of nutrition, providing better housing standards with emphasis on space and equipment used, and intensifying daily checks of animals.
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