Molecular imaging advances our understanding of cellular and molecular functions within complex biological systems. The development of novel imaging probes that can be applied to answer fundamental biological questions, diagnose and monitor disease progression and the efficacy of therapy in vivo is essential to the field of molecular imaging. Bioluminescence imaging is a powerful technique that allows to study and follow biological processes of interest noninvasively in real-time in living animals. Activatable bioluminescent probes can be designed according to the target of interest and can provide imaging signal in response to the specific stimuli. A strategy called "caged luciferin" can be used to design new bioluminescent probes for imaging of enzymatic activity, the presence of small molecules or metabolite uptake in vivo. In Chapter 1 we present an overview of bioluminescence imaging, with a focus on firefly luciferase-luciferin system. The caged luciferin approach is discussed and examples of existing caged luciferin probes are presented. In Chapter 2 we describe the development of a bioluminescent probe for imaging of bacterial nitroreductase activity and show the potential for its application in different areas of research. Bacterial nitroreductases have been widely utilized in the gene-directed enzyme prodrug therapy (GDEPT) approach for cancer therapy that reached clinical trials. However, both preclinical and clinical development of NTR-based GDEPT systems has been hampered by the lack of imaging tools that allow in vivo evaluation of transgene expression. We developed the NTR caged luciferin (NCL) probe and demonstrated its application for sensitive bioluminescence imaging of NTR in vitro, in bacteria and cancer cells, as well as in vivo in mouse models of bacterial infection and NTR-expressing tumor xenografts. We anticipate that this probe would significantly accelerate the development of cancer therapy approaches based on GDEPT and other fields where evaluation of NTR expression is important. In Chapter 3 we describe the development of a bioluminescent probe for imaging of hydrogen sulfide (H2S) using the caged luciferin approach. The objective of the research was to develop a probe that can detect endogenously produced H2S noninvasively in real-time in living animals. We present a series of caged luciferin probes that were evaluated on their ability to rapidly and selectively detect H2S in in vitro assays, in cells and in bacterial culture. The two selected probes were applied for imaging of exogenous H2S in the gastrointestinal tract in living mice. We anticipate further applications of the best performing probe (Az-CL) for imaging of H2S production by gut microbiota in mice. In Chapter 4 we present the overall conclusion followed by the outlook and future perspectives.