Embedded devices almost involve every part of our lives, such as health condition monitoring, communicating with other people, traveling, financial transactions, etc. Within the embedded devices, our private information is utilized, collected and stored. Cryptography is the security mechanism within the embedded devices for protecting this secret information. However, cryptography algorithms can still be analyzed and attacked by malicious adversaries to steal secret data. There are different categories of attacks towards embedded devices, and the side-channel attack is one of the powerful attacks. Unlike analyzing the vulnerabilities within the cryptography algorithm itself in traditional attacks, the side-channel attack observes the physical effect signals while the cryptography algorithm runs on the device. These physical effects include the power consumption of the devices, timing, electromagnetic radiations, etc., and we call these physical effects that carry secret information side-channel leakage. By statistically analyzing these side-channel leakages, an attacker can reconstruct the secret information. The manifestation of side-channel leakage happens at the hardware level. Therefore, the designer has to ensure that the hardware design of the embedded system is secure against side-channel attacks. However, it is very arduous work. An embedded systems design including a large number of electronic components makes it very difficult to comprehensively capture every side-channel vulnerability, locate the root cause of the side-channel leakage, and efficiently fix the vulnerabilities. In this dissertation, we developed methodologies that can help designers detect and fix side-channel vulnerabilities within the embedded system design at low cost and early design stage. / Doctor of Philosophy / Side-channel leakage, which reveals the secret information from the physical effects of computing secret variables, has become a serious vulnerability in secure hardware and software implementations. In side-channel attacks, adversaries passively exploit variations such as power consumption, timing, and electromagnetic emission during the computation with secret variables to retrieve sensitive information. The side-channel attack poses a practical threat to embedded devices, an embedded device's cryptosystem without adequate protection against side-channel leakage can be easily broken by the side-channel attack. In this dissertation, we investigate methodologies to build up comprehensive side-channel resistant embedded systems. However, this is challenging because of the complexity of the embedded system. First, an embedded system integrates a large number of components. Even if the designer can make sure that each component is protected within the system, the integration of the components will possibly introduce new vulnerabilities. Second, the existing side-channel leakage evaluation of embedded system design happens post-silicon and utilizes the measurement on the prototype of the taped-out chip. This is too late for mitigating the vulnerability in the design. Third, due to the complexity of the embedded system, even though the side-channel leakage is detected, it is very hard to precisely locate the root cause within the design. Existing side-channel attack countermeasures are very costly in terms of design overhead. Without a method that can precisely identify the side-channel leakage source within the design, huge overhead will be introduced by blindly add the side-channel countermeasure to the whole design. To make the challenge even harder, the Power Distribution Network (PDN) where the hardware design locates is also vulnerable to side-channel attacks. It has been continuously demonstrated by researchers that attackers can place malicious circuits on a shared PDN with victim design and open the opportunities for the attackers to inject faults or monitoring power changes of the victim circuit. In this dissertation, we address the challenges mentioned above in designing a side-channel-resistant embedded system. We categorize our contributions into three major aspects—first, we investigating the effects of integration of security components and developing corresponding countermeasures. We analyze the vulnerability in a widely used countermeasure - masking, and identify that the random number transfer procedure is a weak link in the integration which can be bypassed by the attacker. We further propose a lightweight protection scheme to protect function calls from instruction skip fault attacks. Second, we developed a novel analysis methodology for pre-silicon side-channel leakage evaluation and root cause analysis. The methodology we developed enables the designer to detect the side-channel leakage at the early pre-silicon design stage, locate the leakage source in the design precisely to the individual gate and apply highly targeted countermeasure with low overhead. Third, we developed a multipurpose on-chip side-channel and fault monitoring extension - Programmable Ring Oscillator (PRO), to further guarantee the security of PDN. PRO can provide on-chip side-channel resistance, power monitoring, and fault detection capabilities to the secure design. We show that PRO as application-independent integrated primitives can provide side-channel and fault countermeasure to the design at a low cost.