Resistance to gastro-intestinal (GI) nematode infection in sheep may be partly attributed to host genetic variation. Faecal egg count (FEC) of an individual is an important indicator trait that measures the relative resistance of sheep to GI nematode infections. The FEC can be measured easily and repeatedly over short time intervals, and its genetic properties and utility as a selection tool are well understood (Bishop and Stear, 2001). However, FEC is the result of a complex series of host-parasite interactions that depend on host genetics and immunological mechanisms, epidemiology of the disease, and other non-genetic measures. The objective of the present study was to determine, in silico, underlying host immunological mechanisms that could lead to observable major genes for FEC. To achieve that, we have extended the stochastic genetic epidemiological model for nematode infection in sheep as described by Bishop and Stear (2001), and used complex segregation analyses to explore the genetic properties of the simulated FEC data.