A number of folks have asked the question about what they can do in CCDA for Meaningful Use Stage 2 when there are no medications, allergies or problems to report in the document, or when, because MU Stage 2 allows the physician to customize the content.
This is an interesting question. MU Stage 2 says you have to provide the content for 17 different data elements, but it doesn't specifically say what you do when that isn't present. Certified products have to pass tests which verify that they can create the data elements, but those tests at present DO NOT verify that they've correctly produced a CCDA document where there is no data for a medications, labs, allergies or problems section. But clearly this can happen, and CCDA has allowed for it, although it is missing good examples (that's a work stream happening in the Structured Documents Example Document task force)
My recommendation is to supply the empty section with an appropriate flavor of null for the entry that would be required in that section. You can find some information above in my various posts on moving from C32 to CCDA. This needs to be addressed better in future certification and regulation.
These would be valid instances of a CCDA for Meaningful Use, but using them won't get you certified. In other words, what you have to do for certification is everything. What you have to do in the real world is report the data that you have, or in some cases, report that you don't have that data to report.