Side-channel attacks have become a severe threat to the confidentiality of computer applications and systems. One popular type of such attacks is the microarchitectural attack, where the adversary exploits the hardware features to break the protection enforced by the operating system and steal the secrets from the program. In this paper, we systematize microarchitectural side channels with a focus on attacks and defenses in cryptographic applications. We make three contributions. (1) We survey past research literature to categorize microarchitectural side-channel attacks. Since these are hardware attacks targeting software, we summarize the vulnerable implementations in software, as well as flawed designs in hardware. (2) We identify common strategies to mitigate microarchitectural attacks, from the application, OS and hardware levels. (3) We conduct a large-scale evaluation on popular cryptographic applications in the real world, and analyze the severity, practicality and impact of side-channel vulnerabilities. This survey is expected to inspire side-channel research community to discover new attacks, and more importantly, propose new defense solutions against them.