Organic based dyes that exhibit fluorescence property have been explored in medical field. The growing evidences suggest that Near Infrared based squaraine dyes serve as a valuable resource for diagnosing medical related problems. Squaraine dyes are unique class of dyes that exhibit intense absorption and emission characteristics in the near infrared region with good stability and optoelectronic properties thereby making them more suitable for a number of state of art applications including solar cells, data storage, photoconductivity and diagnosis of medical related problems. They generally possess an aromatic four membered ring system with zwitterionic structure in which the electrons are highly delocalized over the conjugated bridge. In this review, with a brief introduction to the synthesis of these class of squaraine dyes, their role in bioimaging, as chemosensors and cancer detection are discussed. Additionally, future perspectives and challenges are also presented.