High pathogenicity avian influenza (HPAI) is an acute infectious disease of poultry and wild birds that has been occurring worldwide and has been controlled in many countries by culling birds on farms with disease outbreaks. We compared the gross lesions observed in influenza A (H5Nx) virus-positive cases of chickens and ducks in South Korea between 2023 and 2025. A total of 49 outbreaks were identified, comprising 34 cases in chickens and 15 cases in ducks, with both H5N1 and H5N6 subtypes detected. The lesions observed most frequently in chickens included splenomegaly and splenic necrosis, followed by tracheal congestion and pancreatic necrosis. In ducks, tracheal congestion was the most common lesion, followed by pancreatic necrosis and splenomegaly; hemorrhage and/or necrosis were also observed in the liver, ovarian follicles, heart, and lungs. Gross lesions in poultry caused by the H5N1 virus during the 2024–2025 season were observed more frequently than those associated with H5N6 virus in 2023. HPAI cases were characterized by ≥2 HPAI-typical lesions, such as pancreatic necrosis, splenic necrosis, and ovarian follicular hemorrhage, or the presence of HPAI–associated lesions in ≥3 different organs, even in the absence of HPAI-typical lesions. Assessing gross lesions in HPAI cases is crucial for guiding immediate disease control measures, including imposing movement restrictions on suspected farms, while awaiting confirmation by genetic testing and sequencing.