This paper describes a secure data collection infrastructure involving standardized electronic medical record (EMR) storage and Private Set Intersection, a secure data collection technology based on Bloom filter. The objective of this infrastructure is to facilitate rapid secondary use of exported EMR data in cross-patient or cross-institutional analyses based on the Standardized Structured Medical Information eXchange (SS-MIX), Japan's domestic standard for EMR exporting. Design of the infrastructure and its underlying concepts are described herein. In an experimental test, an intersection operation involving approximately 1 million records was completed within a minute; this result is expected to be representative of the system in actual use. In forthcoming work, we plan to verify the system performance using larger data sets.