Adoption of electronic clinical data exchange (CDE) across disparate healthcare organizations remains low in community settings despite demonstrated benefits. To expand CDE in communities, New York State funded sixteen community-based organizations to implement point-to-point directed exchange (n=8) and multi-site query-based health information exchange (HIE) (n=8). We conducted a cross-sectional study to compare adoption of directed exchange versus query-based HIE. From 2008 to 2011, 66% (n=1,747) of providers targeted for directed exchange and 21% (n=5,427) of providers targeted for query-based HIE adopted CDE. Funding per provider adoptee was almost two times greater for directed exchange (median (interquartile range): $25,535 ($17,391-$42,240)) than query-based HIE ($14,649 ($9,897-$28,078)), although the difference was not statistically significant. Because its infrastructure can cover larger populations using similar levels of public funding, query-based HIE may scale more broadly than directed exchange. To our knowledge, this is among the first studies to compare directed exchange versus query-based HIE.