I'm analyzing a data base from an ecological study and I'd like to read a good reference book about this kind of studies as there are some limitations concerning their analysis; for example, they are susceptible to ecological fallacy.
I don't know that there is necessarily a book on ecological studies, but there are some decent articles written about it. I'd consider starting with the January 2012 issue of Epidemiology, Vol. 23 No. 1. The reason for this is two articles:
Radon and Skin Cancer in Southwest England: An Ecologic Study by B. Wheeler et al. Commentary: A Niche for Ecologic Studies in Environmental Epidemiology by D. Savitz
The reason for this is as follows: The first is an actual ecologic study, on your area of interest, that was good enough to make it into one of the best epidemiology journals published. If you're going to do an ecologic study, there are far worse templates to work off of. The second is a commentary on that study, outlining when and where ecologic studies have a place to contribute to the literature, and where their drawbacks overwhelm their utility.
There's also a chapter on ecologic studies in Modern Epidemiology 3rd Edition by Rothman, Greenland and Lash. This is one of the definitive reference books for the entire field, and if you're conducting any type of epidemiological study, a reference you should own.