Vaccine against foot-and-mouth disease (FMD) is prepared after inactivating the virus produced in cell culture. Inactivation of the FMD virus (FMDV) was earlier done by formaline. However, several vaccine outbreaks, which occurred in Europe revealed that the formaline treatment is not highly effective for virus inactivation. Subsequently, binary ethyleneimine (BEI) was identified as an effective inactivation reagent for FMDV. However, these chemical reagents are likely to have effect on whole virus particle whose integrity is essential for vaccine potency. Therefore, a need is felt to develop non-chemical methods. We have studied induction of endonucleolytic activity as an alternative method for virus inactivation. This method of inactivation was compared with the chemical methods, and found to be highly effective for virus inactivation. The effects of endonucleolytic activity on the integrity of virus capsid was studied using antibodies raised against recombinant proteins, which elicited antibodies against major epitopes present on the surface of the virus. Further, the effect of the agents on the integrity of the virus capsid was studied by using antigen capture PCR (Ag-RT/PCR) which detects the whole virus. The studies showed that inactivation of the virus by induction of endonucleolytic activity is more effective besides maintaining virus integrity. The effect of various inactivating agents on four serotypes of FMDV has also been studied and found to have varying effects, depending on serotype. © 2002 Elsevier Science Ltd. All rights reserved.