Objective: Cupressaceae pollen has commonly been reported to be an important aeroallergen and causal factor of spring, autumn and winter pollinosis in many countries. The aim of this study was to compare of the structure and allergenic protein content of Cupressus arizonica Greene., Cupressus sempervirens L. and Juniperus oxycedrus L. pollen in detail and contribute to Cupressaceae pollen allergen diagnosis and therapy studies in Turkey.,Methods: The pollen structure were examined by LM and SEM. Pollen protein content was investigated by Bradford protein assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blot analysis and two-dimensional polyacrylamide gel electrophoresis (2DE PAGE), respectively. Pectate lyase (PL) enzyme activities were compared. Immunoblotting was carried out by using extracts of the three taxa pollen collected from Turkey.,Results: All three taxa was found very similar in terms of pollen morphology however, intine thickness was prominently different. Cupressus arizonica pollen extracts showed the lowest PL activity. Five sera specific IgE of all allergic subjects showed reaction with only C. arizonica pollen extracts.,Conclusions: As a conclusion, the pollen structure, protein function or protein structure and isoforms of allergens could affects allergenic properties of the pollen. This study also may help to improve the Cupressaceae pollen allergen diagnosis and therapy.