Abstract Pteropid bats are species of zoonotic significance and are known to be reservoir hosts of many viral diseases recently emerged in Asia and Australia. The transfer of these organisms from bats into terrestrial hosts resulted in lethal illnesses in humans and animals. Implementing attentive strategies for the detection and monitoring of these organisms is essential to the protection of humans, animals and the balance of the global economy. Unfortunately the paucity of information on these mammals’ immune system and the absence of diagnostic tools for the detection and for the studying of the humoral response in these animals disengage us from responding promptly when such outbreaks occur and prevent us from describing the possible underling causes that may be responsible for the absence of symptoms in bats infected with such organisms. It was assumed that flying foxes have immunoglobulin like molecules that provide humoral response and are involved in mediating secondary effector functions such as complement fixation and activation of other components of the cellular response in a similar manner as it occurs in humans and other mammals. The aims of this study which include immunoglobulin isotype identification, purification and characterisation as well as generation of reagents that are immunoglobulin class specific, provide the primary platform that should enable us to begin examining these questions. IgG was purified from the black flying fox’s serum by affinity chromatography using Protein G and Protein A. Protein L was ineffective in purifying any antibody from the bat serum. The heavy chain of IgG was also purified by gel electroelution. IgG was digested with papain to yield Fab and Fc fragments. The identity of the bat IgG was confirmed by N-terminal sequencing of the heavy chain and light chain of immunoglobulins separated by SDS-PAGE and by N-terminal sequencing of Fc and Fc' fragments. IgM has also been purified using methods that have not been previously explored to our knowledge. These methods consisted of the purification of Fab specific antibodies from antisera generated against Fab, and using these antibodies to capture other immunoglobulin classes in samples that had been previously enriched by classical fractionation methods. Antisera against the whole IgG molecule, Fc, Fab, IgG heavy chain and IgM heavy chain have been produced in rabbits and tested by Western blot and ELISA. The antisera against the whole IgG molecule and against the Fc were also utilized to detect antibodies to Nipah virus in bats that were found positive to Serum Neutralisation Test. Failure to identify the bat IgA in the bat serum poses questions on the presence, abundance and functional significance of such molecule in bats. The tools that were generated in this study recognise immunoglobulin isotypes, which enabled us to detect and measure antibodies and will allow the study of the humoral response in infected bats to a large extent. Tedious approaches routinely adopted for the purification of antibodies involve a series of pre-fractionation steps or affinity chromatography which rely on the use of expensive immobilised novel or partially characterised ligands, with no guarantee of affinity for the immunoglobulin isotype of interest. The method adopted for immunoglubulin isotype purification described in this study proved to be an effective, reasonably quick and economic solution for immunoglubulin isotype purification from any mammalian species.