Addressing host-microbe interactions through immune responses in out bred species is limited by the need to use replicates to overcome genetic variance and issues associated with conducting studies in multiple environments. In order to overcome these issues, we initiated a study to determine the intrinsic immune response variance in cloned pigs during development and under various challenge conditions. Nuclear transfer cloned Duroc gilts were used in a comparison to age- matched Yorkshires littler-mates. To establish intrinsic immune variations, blood samples were drawn to evaluate the animals for certain immunological parameters and individual peripheral blood lymphocyte (PBL) immune responses in vitro to transmissible gastroenteritis virus (coronavirus) (TGE) or a synthetic oligonucleotide containing a CpG motif. Additionally the animals were challenged in vivo with an ascaris antigen, and the allergic response of the animals was determined by skin testing. Our results suggest that clonal quantitative variance is a function of antigenic complexity with environmental factors contributing to the qualitative differences observed.