GL F V 4 Procedure in the case of lack of unity during search

The search division may neither refuse the application for lack of unity nor require limitation of the claims, but must inform the applicant that, if the search report is to be drawn up to cover those inventions present other than the first mentioned, then further search fees must be paid within two months. This applies even if the search reveals prior art that renders the entire subject-matter of the first invention not novel.[Rule 64(1); Rule 64(2); ]
When lack of unity is raised a posteriori, the assessment of the search division is provisional (G 2/89) and is based on the prior art at hand when the assessment is done. In view of the fact that such novelty and inventive step considerations are being made without the applicant having had an opportunity to comment, the search division will exercise restraint in this assessment and in borderline cases, will preferably refrain from considering an application as not complying with the requirement of unity of invention.
Before issuing an invitation to pay additional fees based on an a posteriori assessment (see B‑VII, 1.2), the search division will assess the technical problem underlying a claimed group of inventions in the light of both the disclosure of the application as a whole and the relevant prior art at hand revealed by the search (see W 6/97, W 6/91).
The consideration of the requirement of unity of invention is always made with a view to giving the applicant fair treatment and the invitation to pay additional fees is made only in clear cases.
The applicant is never invited to pay an additional search fee for claimed inventions that are either not novel or do not possess an inventive step over the prior art at hand. Nevertheless, the search division may still raise an objection of lack of unity for such alleged "sub-inventions" in view of potential amendments that could be reasonably expected in the light of the description and any drawings.
However, if the inventions concern non-obvious alternatives to the disclosure of the prior art at hand or technical details of different apparatuses/‌methods/‌products that require a complete new search for an enabling disclosure, the search division may invite the applicant to pay additional fees for all the inventions.
Example: 
The independent claim is directed to a new method to dope a molecule so as to enhance its ability to bind to a cellular membrane's receptor. A dependent claim claims that the molecule can be doped to bind to several different receptors of the membrane. The search reveals that the method of the independent claim, applied to one receptor listed in the dependent claim, has already been disclosed in the prior art. If the search division is of the opinion that the application of the by now known method to the alternative receptor is an invention in view of the prior art at hand, it invites the applicant to pay additional fees for all the remaining alternatives since a complete search needs to be carried out in order to try to retrieve an enabling disclosure for each of them.

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EPC Implementing Rules

EPO Guidelines - B Search

EPO Guidelines - C Procedureal Aspects of Substantive Examination

EPO Guidelines - F The European Patent Application

Case Law of the Enlarged Board

General Case Law