The search and examination phases constitute the main part of the prosecution of a patent application leading to grant or refusal.

A search is conducted by the patent office for any prior art that is relevant to the application in question and the results of that search are notified to the applicant in a search report. Generally the examiner conducting the search indicates in what aspect the documents cited are relevant (novelty, inventive step, background) and to what claims they are relevant. The materials searched vary depending on the patent office conducting the search, but principally cover all published patent applications and technical publications. The patent office can provide a preliminary, non-binding, opinion on patentability, to indicate to the applicant its views on the patentability and let the applicant decide how to proceed at an early stage.

The search report is typically published with the patent application, 18 months after the earliest priority date, or if it is not available at that time it is published once it is available.

The examination of patent applications may either be conducted at the same time as the search (as in the US, where a search report is not issued), or at a later date after the Applicant has requested examination.

Examination is the process by which a patent office determines whether a patent application meets the requirements for granting a patent. The process involves considering whether the invention is novel and inventive, whether the invention is in an excluded area and whether the application complies with the various formalities of the relevant patent law.

If the examiner finds that the application does not comply with requirements, an examination report (Office action in the US) is issued drawing the examiner's objections to the attention of the applicant and requesting that they be addressed. The applicant may respond to the objections by arguing in support of the application, or making amendments to the application to bring it in conformity. Alternatively, if the examiner's objections are valid and cannot be overcome, the application may be abandoned.

The process of objection and response is repeated until the patent is in a form suitable for grant, the Applicant abandons the applications, or a hearing is arranged to resolve the matter.

The rate at which patent applications are allowed can vary significantly from one technology to another. US patent applications in the field of electrical connectors, for example, get one allowance for every two rejections. Business method patent applications, however, only get one allowance for every 20 rejections.

In some jurisdictions, substantive examination of patent applications is not routinely carried out. Instead, the validity of invention registrations is dealt with during any infringement action.

The search and examination process is principally conducted between the patent office and the applicant. However, in some jurisdictions, it is possible for interested third parties to file opinions on the patentability of an application. Such opinions may take the form of a formal pre-grant opposition inter partes procedure or it may simply be an opportunity of filing observations as a third party. Reform legislation is set to create an opposition system in the United States.

An applicant is free to abandon an application during the search and examination process. An application may be abandoned if, for example, prior art is revealed which will prevent the grant of a patent and the applicant decides to save cost by terminating the application. An application may be deemed abandoned by the patent office if the applicant fails to meet any of the requirements of the application process, for example replying to an examination report.