Modern crimes such as terrorism, money laundering and illegal immigration are majorly committed by individuals who falsify their identities by forging identification documents. One such document that is a target of forgery in Kenya is the national identity card. Research has shown that thousands of national identity cards in use today are not genuine. An understanding of the challenges that make identity card systems vulnerable to fraud may help in developing specifications for secure identification systems. This study investigates design and functional weaknesses inherent in Kenya’s national identity card system and proposes potential areas for further research. A survey was carried out on Kenya’s second generation identity card system which is currently run by the department of National Registration Bureau. System administrators and users of Civil Identification System, Automatic Fingerprint Identification System and Production System were interviewed. In addition, all processes undertaken at the field registration stations were observed and relevant documentation studied. The study found out that the national identity card system is challenged mainly by existing manual processes, outdated technology and its architectural design. It is hoped that the findings of this study will assist relevant experts in developing effective national identity card systems.