This paper presents results concerning the traceability of a secure data collection infrastructure based on the Bloom Filter involving standardized electronic medical record (EMR) storage. 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 export. Secondary use of EMR data should be based on the principle of patient consent. Therefore, securing the traceability of patient EMR data is important for achieving reliable data collection systems for secondary use. Blockchain is a strong candidate, and we evaluated its performance using several implementations. As shown by the evaluation, it is difficult to realize the method of recording the query history of secondary use on the blockchain. We thus propose a method for recording index information of distributed log data.