Carbonyl-ligation reactions are considered to be largely biorthogonal due to the rarity of ketones and aldehydes in normal mammalian biology, especially in the extracellular space. However during development, in wound healing, or in response to many disease conditions, certain extracellular matrix (ECM) proteins can be post-translationally modified by lysyl oxidases to contain aldehyde bearing side chains. In many diseases, accelerated ECM production is a part of a process called fibrosis (scarring of tissue), and about half the deaths in the industrialized world arise from disease with a fibrotic component. During fibrogenesis (active fibrosis), lysyl oxidases are upregulated, catalyzing the oxidation of lysine residues on ECM proteins to form lysine aldehyde (allysine, LysAld). LysAld undergoes condensation reactions with other LysAld or Lys residues of adjacent collagens to crosslink proteins. Despite the centrality of fibrogenesis in development and in so many diseases, there is a general lack of tools to noninvasively detect and quantify fibrogenesis in humans or in animal models. Here I will describe the rational design of molecular probes for LysAld to enable detection, staging, and treatment monitoring of fibrogenesis using MRI, PET, or fluorescence imaging. I will describe in vitro and in vivo validation of the LysAld targeting probes and their applications in a wide range of diseases. To increase the sensitivity of LysAld probes, we systematically optimized probe structures to modulate the kinetics of aldehyde condensation and hydrolysis reactions, molecular hydrophilicity, pharmacokinetics and elimination. Combining these strategies with signal amplification by designing “on-off” probes, we extended the probe applicability from organs of high LysAld levels (lung) to low-concentration systems (liver, tumor, and cardiac tissues). Reducing the hydrolysis rate of the probe-LysAld adduct extended the imaging window and permitted specific detection of LysAld in the kidneys. Importantly, our design strategies demonstrate multi-modal compatibility, validated through magnetic resonance imaging, positron emission tomography and fluorescence imaging platforms. The multi-scale detection capability in different imaging modalities (cellular to in vivo) provides critical spatial-temporal insights into fibroproliferative disease dynamics in different species and tissues, including onset, progression, and therapeutic response.