With increased growth of the Internet of Things (IoT) and physical exposure of devices to adversaries, a class of physical attacks called side-channel analysis (SCA) has emerged which compromises the security of systems. While security claims of cryptographic algorithms are based on the complexity of classical cryptanalysis attacks, they exclude information leakage by implementations on hardware platforms. Recent standardization processes require assessment of hardware security against SCA. In this dissertation, we study SCA based on deep learning techniques (DL-SCA) as a universal analysis toolbox for assessing the leakage of secret information by hardware implementations. We demonstrate that DL-SCA techniques provide a trade-off between the amount of prior knowledge of a hardware implementation and the amount of measurements required to identify the secret key. A DL-SCA based on supervised learning requires a training set, including information about the details of the hardware implementation, for a successful attack. Supervised learning has been widely used in power analysis (PA) to recover the secret key with a limited size of measurements. We demonstrate a similar trend in fault injection analysis (FIA) by introducing fault intensity map analysis with a neural network key distinguisher (FIMA-NN). We use dynamic timing simulations on an ASIC implementation of AES to develop a statistical model for biased fault injection. We employ the model to train a convolutional neural network (CNN) key distinguisher that achieves a superior efficiency, nearly $10times$, compared to classical FIA techniques. When a priori knowledge of the details of hardware implementations is limited, we propose DL-SCA techniques based on unsupervised learning, called SCAUL, to extract the secret information from measurements without requiring a training set. We further demonstrate the application of reinforcement learning by introducing the SCARL attack, to estimate a proper model for the leakage of secret data in a self-supervised approach. We demonstrate the success of SCAUL and SCARL attacks using power measurements from FPGA implementations of the AES and Ascon authenticated ciphers, respectively, to recover entire 128-bit secret keys without using any prior knowledge or training data. / Doctor of Philosophy / With the growth of the Internet of Things (IoT) and mobile devices, cryptographic algorithms have become essential components of end-to-end cybersecurity. A cryptographic algorithm is a highly nonlinear mathematical function which often requires a secret key. Only the user who knows the secret key is able to interpret the output of the algorithm to find the encoded information. Standardized algorithms are usually secure against attacks in which in attacker attempts to find the secret key given a set of input data and the corresponding outputs of the algorithm. The security of algorithms is defined based on the complexity of known cryptanalysis attacks to recover the secret key. However, a device executing a cryptographic algorithm leaks information about the secret key. Several studies have shown that the behavior of a device, such as power consumption, electromagnetic radiation and the response to external stimulation provide additional information to an attacker that can be exploited to find the secret key with much less effort than cryptanalysis attacks. Hence, exposure of devices to adversaries has enabled the class of physical attacks called side-channel analysis (SCA). In SCA, an attacker attempts to find the secret key by observing the behavior of the device executing the algorithm. Recent government and industry standardization processes, which choose future cryptographic algorithms, require assessing the security of hardware implementations against SCA in addition to the algorithmic level security of the cryptographic systems. The difficulty of an SCA attack depends on the details of a hardware implementation and the form of information leakage on a particular device. The diversity of possible hardware implementations and platforms, including application specific integrated circuits (ASIC), field programmable gate arrays (FPGA) and microprocessors, has hindered the development of a unified measure of complexity in SCA attacks. In this research, we study SCA with deep learning techniques (DL-SCA) as a universal methodology to evaluate the leakage of secret information by hardware platforms. We demonstrate that DL-SCA based on supervised learning can be considered as a generalization of classical SCA techniques, and is able to find the secret information with a limited size of measurements. However, supervised learning techniques require a training set of data that includes information about the details of hardware implementation. We propose unsupervised learning techniques that are able to find the secret key even without knowledge of the details of the hardware. We further demonstrate the ability of reinforcement learning in estimating a proper model for data leakage in a self-supervised approach. We demonstrate that DL-SCA techniques are able to find the secret information even if the timing of data leakage in measurements are random. Hence, traditional countermeasures are unable to protect a hardware implementation against DL-SCA attacks. We propose a unified countermeasure to protect the hardware implementations against a wide range of SCA attacks.