The Protocol to the Comprehensive Nuclear Test-Ban Treaty is divided into three parts. Part I is titled "The International Monitoring System and International Data Centre Functions," Part II is titled "On-Site Inspections," and Part III is titled "Confidence-Building Measures." All three Parts of the Protocol provide procedures to be used in the implementation of the Treaty.

Part I of the Protocol provides details on the IMS and the IDC of the Technical Secretariat and also elaborates on the basic rights and obligations of the States Parties regarding the IMS and the IDC. Part I also provides information on IDC standard products, IDC services to States Parties, national event screening, and technical assistance.

Part II of the Protocol provides detailed information on the procedures for the on-site inspection regime of the Treaty, including the designation of inspectors, points of entry for the inspection team, the on-site inspection request, and privileges and immunities of the inspection team. Article IV, Section D of the Treaty provides the basic rights and obligations of the States Parties under the on-site inspection regime.

Part III of the Protocol provides details on confidence-building measures of the Treaty. These measures are not mandatory and are to be carried out on a voluntary basis by the States Parties. The confidence-building measures that are provided for in Part III include notification of chemical explosions of 300 metric tons, or greater, TNT-equivalent, and invitations to representatives of the Technical Secretariat and States Parties to visit a State Party's territory. Article IV, Section E of the Treaty contains the undertaking by each State Party to cooperate with the Organization and States Parties to implement the measures as set out in Part III.