The main goal in modern biomedicine is to develop specific diagnostic and therapeutic agents for different diseases. Especially in cancer research tumor targeted molecules are the key factor in the development of new anti-tumor drugs. In addition, the early diagnosis of the disease is an important factor for a successful therapy. Synthetic peptides have been shown to be specific targeting agents for next generation diagnostic and therapeutic agents. Noninvasive in vivo imaging using targeting molecules provides modern method for the diagnosis of the pathological alterations like cancer. To evaluate the usefulness of a synthetic peptide for in vivo diagnostic purposes the preclinical biodistribution and targeting studies are essential. Today the widely used preclinical imaging modalities for the biodistribution and tissue alteration studies in experimental animals are single photon emission computed tomography (SPECT) and magnetic resonance imaging (MRI). Together with conventional histochemistry, the biodistribution and tissue/cell location can be determined. In this chapter we describe the conjugation and labelling methods of the peptides for histochemistry and for the molecular imaging with SPECT and MRI modalities.