The PCT‑EPO Guidelines follow the structure of the EP Guidelines (Parts A, B, C, E, F, G and H, without D because there is no opposition, limitation or revocation under the PCT), and as far as possible the organisation within each part is similar to that of the EP Guidelines, adapted to the particularities of the PCT system. The sequence of chapters within Part A, however, differs from that of the EP Guidelines. This is due to the particular way in which the content is being gradually extended and the structure may be reconsidered prior to completion of Part A.

Thus, these Guidelines comprise the following seven parts:

Part E deals with procedural matters relevant to several or all of the stages in procedure at the EPO as PCT Authority. Part F deals with the requirements which the application must fulfil other than patentability, in particular unity of invention (Rule 13 PCT), sufficiency of disclosure (Art. 5 PCT), clarity (Art. 6 PCT) and the right to priority (Art. 8 PCT). Part G deals with excluded subject-matter (Art. 17(2)(a)(i) PCT and Rule 39 PCT; Art. 34(4)(a)(i) PCT and Rule 67 PCT), novelty (Art. 33(2) PCT), inventive step (Art. 33(3) PCT) and industrial application (Art. 33(4) PCT). Part H deals with the requirements relating to amendments and corrections. It relates in particular to the right to amend, the allowability of amendments and the correction of defects and errors.

Each part of the Guidelines is divided into chapters, each subdivided into numbered sections which may be further divided into subsections. Cross-references to other sections and subsections are in the format GL/PCT‑EPO, followed by the relevant letter of that part, then the chapter number (a Roman numeral) and then the section or subsection number (thus, e.g. GL/PCT‑EPO C‑V, 4.2, would be used to refer to subsection 4.2 of chapter V of Part C of the PCT‑EPO Guidelines). When referring to the Guidelines for Examination in the EPO, the same format is used, but with "GL/EPO" instead of "GL/PCT‑EPO".

Marginal references to articles and rules without further identification relate to the Articles or Rules of the Patent Cooperation Treaty which provide authority for what is stated. It is believed that such references avoid the need for extensive quotation from the PCT itself. References to Articles or Rules of the European Patent Convention are followed by "EPC".

Marginal references to the RO and ISPE Guidelines relate to the corresponding sections in those Guidelines and are an indication that the present Guidelines apply within the framework of the RO and ISPE Guidelines, in conformity with the supplementary role of the EPC in the international phase.[Art. 150(2) EPC; ]

Where the practice for EP and PCT applications is the same (e.g. for the assessment of novelty), cross-references are made to the EP Guidelines. Where the practices are only partially overlapping, the information is contained in full in the PCT‑EPO Guidelines, in order to avoid possible confusion. Chapter 3, Annex I, provides an EPC-PCT concordance table.