In environmental health research, a community-based participatory research (CBPR) approach can effectively involve community members, researchers, and representatives from nonprofit, academic, and governmental agencies as equal partners throughout the research process. The authors sought to use CBPR principles in a pilot study; its purpose was to investigate how green construction practices might affect indoor exposures to chemicals and biological agents. Information from this pilot informed the development of a methodology for a nationwide study of low-income urban multifamily housing. The authors describe here 1) the incorporation of CBPR principles into a pilot study comparing green vs. conventionally built urban housing, 2) the resulting implementation and reporting challenges, and 3) lessons learned and implications for increased community participation in environmental health research.