Quantum key distribution (QKD) allows two distant parties to share secret keys with the proven security even in the presence of an eavesdropper with unbounded computational power. Recently, GHz-clock decoy QKD systems have been realized by employing ultrafast optical communication devices. However, security loopholes of high-speed systems have not been fully explored yet. Here we point out a security loophole at the transmitter of the GHz-clock QKD, which is a common problem in high-speed QKD systems using practical band-width limited devices. We experimentally observe the inter-pulse intensity correlation and modulation patterndependent intensity deviation in a practical high-speed QKD system. Such correlation violates the assumption of most security theories. We also provide its countermeasure which does not require significant changes of hardware and can generate keys secure over 100 km fiber transmission. Our countermeasure is simple, effective and applicable to wide range of high-speed QKD systems, and thus paves the way to realize ultrafast and security-certified commercial QKD systems.npj Quantum Information (2018) 4:8 ; doi:10.1038/s41534-017-0057-8 INTRODUCTION Quantum key distribution (QKD) 1-3 allows two legitimate parties, Alice and Bob, to establish symmetric keys with the proven security even in the presence of an eavesdropper, Eve, who has unbounded computational power. Thanks to this unique feature, referred to as "information theoretic security", QKD, combined with Vernam's one-time pad cipher, enables the everlasting protection of confidentiality of data transmission, and hence must be an essential element to construct a long-term security system which cannot be realized only by cryptographic schemes based on computational security. Such a system has been exemplified in the literatures 4,5 as a long-term secure storage network consisting of secret sharing, QKD and authentication schemes to deal with highly confidential data such as personal biomedical data, pharmaceutical, and genetic information. Because of growing interest in the confidentiality of those data, this storage network could be one of the killer applications of QKD.Toward its practical realization, tremendous progress has been made during the past decades. Metropolitan QKD networks have been successfully deployed 6-10 and is going to be a continental scale. 11 To provide information theoretically secure keys to real applications securely and seamlessly, an efficient key management system and application program interfaces have been developed. 12 For the QKD device itself, high-speed and stable operation is critical. By employing the ultrafast optical communication devices, high-speed QKD systems stably operated at GHzclock frequency is realized in the installed fiber networks. [13][14][15] Nevertheless, there remains an obstacle that makes the potential users hesitate to adopt this emerging technology; they would not innovate their existing secure communication systems unless convinced that a QKD system at hand is really secure. I...