Japanese Committee for Clinical Laboratory Standards (JCCLS) and the Japan Accreditation Board for Conformity Assessment (JAB) have developed an accreditation program for clinical laboratories using ISO 15189 in Japan. On October 1, 2004, twelve clinical laboratories applied for trial accreditation assessment. Seven laboratories were selected, including a university hospital laboratory, two other hospital-based laboratories, three large private clinical laboratories and an other private clinical laboratory. JAB had given a one week-training course to the candidate technical assessors who were nominated from the Japanese Society of Laboratory Medicine (JSLM) and the Japanese Association of Medical Technologists (JAMT), and candidate system assessors who were nominated from JAB. Thirty-five members had successfully passed the examination. During the period from November 2004 to May 2005, five laboratories were visited for assessment by four to six assessors for two or three days. Final assessment reports were discussed by the program developing committee for the validation of the accreditation program. The conclusions were that the program did not have any critical problems, but the assessment visit would have been more efficient if JAB published an easily understandable guidance document on ISO 15189, and had some training courses for laboratories in Japan in order to understand ISO 15189 more deeply. In addition, JAB should develop a more simplified checklist, mainly describing the important requirements. JAB formally started the clinical laboratory accreditation scheme from August 1, 2005 and five laboratories were accredited by the newly started accreditation committee on August 31, 2005, and four laboratories were additionally accredited on November 28, 2005. The most difficult clauses in ISO 15189:2003 were 5.6.2 and 5.6.3 on uncertainty and traceability, and 5.7.1 on post-examination procedures. Some difficult clauses to understand in the International Standard were discussed.