This book constitutes the proceedings of the 13th International Workshop on Cryptographic Hardware and Embedded Systems CHES 2011 held in Nara Japan from September 28 until October 1 2011. The 32 papers presented together with 1 invited talk were carefully reviewed and selected from 119 submissions. The papers are organized in topical sections named: FPGA implementation; AES; elliptic curve cryptosystems; lattices; side channel attacks; fault attacks; lightweight symmetric algorithms PUFs; public-key cryptosystems; and hash functions.