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The Bennett-Brassard 1984 (BB84) protocol is the most widely implemented quantum key distribution (QKD) scheme. However, despite enormous theoretical and experimental efforts in the past decades, the security of this protocol with imperfect sources has not yet been rigorously established. In this work, we address this shortcoming and prove the security of the BB84 protocol in the presence of multiple source imperfections, including state preparation flaws and side channels, such as Trojan-horse attacks, mode dependencies and classical correlations between the emitted pulses. To do so, we consider a modified BB84 protocol that exploits the basis mismatched events, which are often discarded in standard security analyses of this scheme; and employ the reference technique, a powerful mathematical tool to accommodate source imperfections in the security analysis of QKD. Moreover, we compare the achievable secret-key rate of the modified BB84 protocol with that of the three-state loss-tolerant protocol, and show that the addition of a fourth state, while redundant in ideal conditions, significantly improves the estimation of the leaked information in the presence of source imperfections, resulting in a better performance. This work demonstrates the relevance of the BB84 protocol in guaranteeing implementation security, taking us a step further towards closing the existing gap between theory and practice of QKD.