Semiconducting organic materials based on π-conjugated molecules or polymers have recently received considerable attention for their use as imaging and therapeutic agents for biomedical applications. Because π-conjugated materials exhibit desirable characteristics such as high brightness, photostability, emission tunability, and low toxicity, they are an attractive alternative to conventional fluorophores. In this review, the recent development of π-conjugated molecular nanoparticles for in vitro and in vivo biomedical applications is discussed.