Background To date, studies on loop L1 HVRs1-4 region of the hexon gene in fowl adenovirus genome (FAdVs) lack comprehensive molecular data. In this study detailed prospectively obtained sequences from field adenovirus strains, NVRI, Poland have been analyzed. Methods Overall hundred and thirty seven adenovirus strains were collected, evaluated, and examined of hyper variable loop L1 region HVRs1-4 of the hexon gene for the presence of similarity, mutations, tertiary structure, and spinal conformation. Results Sequences were characterized, and divided for five species and seven types, FAdV-A-E/FAdV-1/2/4/5/7/8a/8b/11. The presence of predicted tertiary structure depending on type/species were determined. Analysis of specific selected sequences: GQMTN 1/A, 7/E, and 8b/E, GQMTT 2/11/D, GQLSN 4/C, GQMTH 5/B, and GQMSN 8a/E in examined HVRs1-4 Loop L1 region of hexon gene compared to tertiary structure indicated that this visibly conservative region represents the antigenic binging activity. Conclusion This is the first molecular study on tertiary structure on HVRs1-4 region in adenovirus genome conducted in Poland. Analysis indicated specific sequence in Loop L1 HVR1-4 region which is strictly responsible for antibodies binding. This information could assist during the process connected with specific preventive strategies based on their molecular genome investigation and new facilitate studies. This study will help to better understand the mechanisms of pathogenicity of adenovirus strains provide a guide for disease control in birds.