Parasites comprise diverse and complex organisms, which substantially impact human and animal health. Most parasites have complex life-cycles, and by virtue of co-evolution have developed multifaceted, often life-cycle stage-specific relationships with the immune system of their hosts. The complexity in the biology of many parasites often limits our knowledge of parasite-specific immune responses, to
in vitro
studies only. The relatively recent development of methods to stably manipulate the genetic make-up of many parasites has allowed a better understanding of host-parasite interactions, particularly
in vivo
. In this regard, the use of transgenic parasites can facilitate the study of immunomodulatory mechanisms under
in vivo
conditions. Therefore, in this review, we specifically highlighted the current developments in the use of transgenic parasites to unravel the host’s immune response to different life-cycle stages of some key parasite species such as
Leishmania
,
Schistosoma
,
Toxoplasma
,
Plasmodium
and
Trypanosome
and to some degree, the use of transgenic nematode parasites is also briefly discussed.