The covalent modifications resulting from chlorine reactions with peptide-bound amino acids contribute to pathogen inactivation and disinfection byproduct (DBP) formation. Previous research suggested that histidine is the third most reactive of the seven chlorine-reactive amino acids, leading to the formation of 2-chlorohistidine, 2-oxohistidine, or low-molecular-weight byproducts such as trihalomethanes. This study demonstrates that histidine is less reactive toward formation of chlorine transformation products (transformation time scale of hours to days) than five of the seven chlorine-reactive amino acids, including tyrosine (transformation time scale of minutes). Chlorine targeted tyrosine in preference to histidine within peptides, indicating that chlorine reactions with tyrosine and other more reactive amino acids could contribute more to the structural modifications to proteins over the short time scales relevant to pathogen inactivation. Over the longer time scales relevant to disinfection byproduct formation in treatment plants or distribution systems, this study identified β-cyanoalanine as the dominant transformation product of chlorine reactions with peptide-bound histidine, with molar yields of ∼50% after 1 day. While a chlorinated histidine intermediate was observed at lower yields (maximum ∼5%), the cumulative concentration of the conventional low-molecular-weight DBPs (e.g., trihalomethanes) was ≤7%. These findings support the need to identify the high-yield initial transformation products of chlorine reactions with important precursor structures to facilitate the identification of unknown DBPs.