When you are ready to build a PDF file, go to the InDesign menu File > Adobe PDF presets > Adobe PDF/X-4. (InDesign CS3 and later versions)

Export Adobe PDF dialog for Coated papers
Go to Output in the menu on the left side; modify ‘Color Conversion‘ to ‘Convert to Destination (Preserve Numbers)‘ and ‘Destination‘ to the profile corresponding to the paper type to be printed on (eg. ISO Coated v2, PSO Uncoated… or ISO Uncoated Yellowish). This will simultaneously change the ‘Output Intent Profile Name‘ to the profile selected.

Uncoated paper

Uncoated yellowish paper
Then please click on the Ink Manager button. Here you can check whether spot colours are used in the document. Unless the printing is to be done with Spot colours (Pantone or similar) or in multiple languages, you should only see 4 colours here. If there are more colours than are to be used in printing, you can tick the ‘All Spots to Process‘ option which will convert all spot colours to CMYK and thus avoid this error in the PDF.

Ink Manager
Under Marks and Bleeds please tick the ‘Crop Marks‘ option and change the offset value to 5.0 mm. If your design requires print to edge you should also modify the bleed area to 10 mm on all sides. You may save these settings as a preset for future use for this printing condition and paper type.

Marks and Bleeds
These settings will create a PDF file in which all RGB data is converted to the selected Output Intent, say ISO Coated v2 (ECI). However, no conversion is done on any CMYK object or image, which is why it is important you pre-convert CMYK files to the correct ICC profile. The output intent makes it easy to verify to which printing condition the PDF file has been produced, thereby eliminating many possible errors.