We recently published a commentary in the American Journal of Public Health describing the concerns we have for protecting study subject anonymity with the use of online geographic and data tools in neighborhood health effects research. Examples of neighborhood data available from these tools include crime statistics from the New York Times and EveryBlock, neighborhood walkability scores from Walkscore.com, restaurant locations from Yelp and geocoding services from Google Maps. These online resources create new opportunities for medical geographic research but also create new ways in which study subject confidentiality can be broken. Typically these web-tools allow a user to enter an address into an online interface and receive back data about the geographic area around that location. We have seen study protocols, training materials, and published papers involving the submission of study subject’s home and/or work addresses to such web services. The broad terms of service on most websites usually permit these service providers to freely use any data passed to them rather than hew to strict rules established by institutional review board (IRB) protocols to protect human subjects. Furthermore, online advertising tracking cookies on the researcher’s (or research assistant’s) browser could be used to release respondent addresses to additional parties without the researcher’s knowledge. In the Commentary we describe approaches to using these online services for neighborhood health effects research while maintaining human subjects protections.