This study aims at assessing the degree of compliance of the Egyptian Phytosanitary (Plant health) organization to the international standards in terms the institutional context; legislative framework, structure and documentation procedures. The assessment contributes to capturing the current situation; identify the gaps in the phytosanitary control system and provide recommendation to overcome these gaps. Identification of gaps can assist in improving the phytosanitary system through improving the relevant organizational behavior. Due to the importance of complying to international standards especially in the agriculture trade arena this study is essential in understanding the key department requiring improvements in the plant health organization. The enhanced compliance of the plant health organization to international standards increases the chances of accessing new markets and maintaining current trade flow and thus increases the national income. Countries deficient in international standards processes and outcomes may not be able to fully trade with world market. Also, deficiencies in application of adequate procedures for imports may cause introduction of exotic pests that would cause destruction to agriculture flora. The Phytosanitary Capacity Evaluation (PCE) model was adopted as the reference measuring the level of compliance with international standards in the Egyptian Phytosanitary System. The study showed that there is clear gap in the legislative and institutional framework of the plant health organization. The compliance according to the responses was 38%, as for the structure reflected in the facilities the compliance was only 25%. The documented procedure in contrary was 72% in compliance with the international standards.