Rapid diagnosis of infectious diseases and appropriate treatment with in time are important steps that promote optimal clinical outcomes and general public health. Today there is large number of new technologies such as nanotechnology, biosensors, and microarray techniques, are being developed and used as diagnostic tools for equine infectious diseases. Nucleic acid based techniques such as polymerase chain reaction (PCR) have become conventional tools in veterinary research and plays an important role in specific typing determinations as well as for rapid screening of ample numbers of samples at the time of equine disease outbreaks. Other biotechnological techniques are populous to be used in the coming times as they can enhance diagnostic efficacy in less time and cost as compared to conventional techniques. This review focuses on biotechnological tools available for equine diseases diagnosis and its applications hold great promise for improving the speed and accuracy of diagnostics for equine infectious diseases.