Introduction: Highly pathogenic avian influenza (HPAI) remains a persistent threat to poultry production systems despite reinforced biosecurity measures. This study aimed to characterize biosecurity deficiencies in HPAI-affected farms in Korea and to identify structured patterns of deficiencies.Methods: Outbreak investigation reports from 311 HPAI-affected farms (2020/2021–2024/2025 seasons) were analyzed, yielding 3,172 biosecurity deficiency records classified into 16 categories across three operational domains. Frequency analysis, k-means clustering, and association rule analysis were applied to identify deficiency patterns and co-occurrence structures.Results: Wildlife control was the most frequent deficiency (85.9%), followed by operational management (65.9%) and deficiencies related to anteroom biosecurity measures in barns (56.3%). Four distinct farm-level deficiency profiles were identified, with significant differences in cluster membership between chicken and duck farms. Association rule analysis revealed consistent co-occurring deficiency pairs, particularly involving farm-entry measures such as visitor and vehicle disinfection.Discussion: These findings indicate that biosecurity deficiencies are not isolated but form structured and interconnected patterns. A system-level approach incorporating targeted, pattern-based biosecurity interventions and risk-based surveillance prioritization may improve the sustainability and effectiveness of HPAI prevention and control in poultry production systems.