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Guide for applicants, Part 2: PCT procedure before the EPO (Euro-PCT Guide)

Lack of unity of invention
If the EPO as ISA considers that the international application claims more than one invention, stating the reasons for its finding it invites the applicant to pay for each further invention an additional search fee, which must be paid direct to the EPO. At the same time the EPO informs the applicant of the result of its partial international search, which is restricted to those parts of the application relating to the invention first mentioned in the claims. 
Art. 2(1).2 RFees
OJ 1989, 61
PCT Newsletter 7/2013, 10 
If the applicant fulfils the requirements for reduction of the search fee, any additional search fee is validly paid upon payment of the reduced amount (see point 213).
If the applicant does not pay any additional search fee, the EPO establishes the ISR and WO-ISA on the basis of the result already communicated. The WO-ISA will contain the reasons for any non-unity objection raised. 
If the applicant pays one or more additional search fee(s) within the time limit set, those parts of the application for which additional search fees have been paid will also be searched. Consequently the ISR and WO-ISA will be established for all inventions for which a search fee has been paid.