Molecular probes for selective identification of biomolecular targets are important to advance our understanding of the molecular mechanisms underlying pathological events and for clinical diagnostic of specific diseases. Luminescent conjugated polythiophenes (LCPs) have been utilized as colorimetric and fluorescent sensing elements for the recording of biological processes, such as DNA-hybridization and ligand-receptor interactions. However, LCPs have several limitations for being used as real time in vivo imaging agents. In this regard, novel thiophene based molecular scaffold, denoted luminescent conjugated oligothiophenes (LCOs) have been developed. The LCOs are chemically defined molecules having distinct side chain functionalizations and a precise number of thiophene units. Properly functionalized LCO showed a striking specificity and selectivity towards distinct molecular targets, such as protein aggregates under physiological conditions. The protein aggregates were easily identified due to the conformation-dependent emission profile from the LCOs and spectral assignment of protein aggregates both in vitro and in ex vivo tissue samples could be obtained. It was also shown that LCOs could be used for live imaging of intracellular molecules and compartments in cells. Overall, we demonstrate that LCOs have the potential of being utilized as powerful practical research tools for studying biological processes in real time.