GA B 27 Non-designation for reasons of national law

For reasons of national law, check-boxes in Box No. V of the PCT request form provide for exceptions to the otherwise automatic designation of Germany (DE), Japan (JP) and the Republic of Korea (KR). Crossing the check-box for these designations is not considered as withdrawal of a designation, but as non-designation of the state(s) concerned.
WIPO PCT Guide 5.053 
According to the national law of these states, the filing of an international application which contains the designation of that state and claims the priority of an earlier national application filed in that state (for Germany: for the same kind of protection) will have the result that the earlier national application ceases to have effect, with the same consequences as the withdrawal of the earlier national application. To avoid this effect, the appropriate box must be crossed (Box No. V PCT request form). More information on so-called "self-designation" can be obtained from the national patent offices concerned. 
As regards the EPC contracting states, the problem of self-designation exclusively concerns Germany (DE), and only if protection via the grant of a national patent in Germany is sought, i.e. if the application actually enters the German national phase. The designation of Germany for the purposes of a European patent is not considered a self-designation and is thus not affected. Consequently, there is no reason for withdrawing the automatic designation of EP.
The national law of a number of EPC contracting states stipulates that, on the basis of a PCT application, only a European patent may be obtained for these states. The countries which close off the route to a national patent in this way were, on 1 January 2018, Belgium (BE), Cyprus (CY), France (FR), Greece (GR), Ireland (IE), Italy (IT), Latvia (LV), Lithuania (LT), Monaco (MC), Malta (MT), Netherlands (NL) and Slovenia (SI).

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EPO Guide for Applicants, part II Int.

EPO Guide for Applicants, part II Int. - A General Overview

EPO Guide for Applicants, part II Int. - B The EPO as a PCT receiving Office

PCT Articles

PCT Implementing Rules