What are the risks of doing a PhD in a new department? I was recently admitted to a doctoral program to be part of their inaugural class for a new interdisciplinary science and engineering department. The program is located at a top-tier university in the United States and appears to be very well funded by the founding university.

The faculty that they have hired so far are all well established researchers in their respective fields. These faculty have also successfully brought the majority of their students and post-docs with them, so there should be no major loss of continuity as far as research is concerned.

My primary concerns are that:


the graduate curriculum itself is new
the program (outside of the reputation of the individual faculty/university itself) is currently not very well known. Will this look bad to prospective employers (both in industry and academic), or is the reputation of my faculty advisor more important?
professors may need to spend more time doing administrative activities for the new department


What other risks are associated with joining a new program, and are there any professional/academic advantages to doing so?
The risks are as you describe, although I suspect that the third item is not as serious (unless your advisor has a formal administrative role). 

The pros are that you will have a lot more input into how the curriculum and the program is shaped. As a new department, people will try things, and not everything will work. There will be many opportunities to suggest improvements and how to do things differently. 

If the parent university is well known, it's in their interest to make sure the new program succeeds, so you should also get some benefit from the level of attention paid by them. By bringing a number of faculty over, they've expressed "buy-in" to the new institute.