Biofunctionalization and manipulating of carbon nanotubes (CNTs) is important for biomedical research and application. Cy5 labeled goat anti-rabbit IgG (anti-IgG-Cy5) is chemically bonded to CNTs via a two-step process of diimide-activated amidation. This process can avoid the intermolecular connection of proteins. Fluorescent imaging of CNTs in aqueous solution has been demonstrated using anti-IgG-Cy5 immobilized CNTs (IgG-CNTs) as the model. The biologically functionalized carbon nanotubes (f-CNTs) in solution have been observed successfully using fluorescence microscopy. The fluorescent image of highly oriented f-CNTs is obtained at first time. The influencing factors on fluorescent imaging including oxidation duration, background noise and reactant concentration are discussed. (C) 2007 Elsevier B.V. All rights reserved.