The core infra-technology in the ubiquitous era, RFID which has taken action from the public institution with the pilot projects as well as the practical projects is gradually extending its spectrum to the private enterprises. Along with its expansion, the audit required on the RFID-based information system is also growing in the industry. Especially, since RFID-based information systems, especially compared to other information systems, are likely to be exposed to many threats, the security audit for them is being emphasized. This paper suggests security audit checking items for the RFID-based information system, which can be used to perform the efficient security audit. The security audit checking items consist of eight basic checking items, each of which consists of detailed review items and can be applied for each building steps of the system(analysis, design, implementation, testing, and development). Finally, this paper confirmed the efficiency of the security audit checking items proposed in this paper through survey by the experienced auditors and analysis of practical audit cases.