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Where can I find out the change in the distribution of religious denominations over time?
One resource is the General Social Survey (GSS). It is a cross-sectional study that has been in existence since 1972. Thus, you can get a view of the changing distribution over the last 35 years (through 2006).
Here's the link to an on-line version of the GSS:
I just looked at RELIG * YEAR and DENOM * YEAR. The relative size of the Protestant population has gone down over time and no-denomination has grown.
I am pointing you to some other resources that are quite good, that may also help you with your question. The Roper Center has a collection of opinion polls, many of which you might not have free access to. However, they have a summary of religious attitudes in "Public Opinion Matters." They have summaries of other hot topics as well, some of which might be useful to you in another project:
The American Religion Archive also provides access to religion-based data:
They provide access to both surveys and a census of religious denominations.
Finally, the Pew Forum on Religion and Public Life has data and reports based on religion and values: