In this study the differential display technique was used to identify differentially expressed genes between a salinomycin-resistant strain of ' Eimeria tenella' and the salinomycin-sensitive Guelph strain. The sporulated oocyst and sporocysts/sporozoites at various times during the process of excystation were used in the study. Since ionophorous compounds primarily affect the invasive sporozoite, this study focussed largely on this stage. Various bands were differentially displayed between the two strains and also during different stages and treatments within the same strain. Variation in individual species of mRNA were observed to occur in the mid to late stages of excystation. Additionally, a differentially amplified fragment was noted between sporozoites of the salinomycin-sensitive Guelph strain and the salinomycin-resistant strain subjected to treatment in PBS and salinomycin. Two cDNA fragments, found to be differentially displayed with the salinomycin-resistant strain of 'E. tenella' sporozoites incubated in PBS were isolated and cloned. Northern blot analysis revealed that the expression of a 1.5 kb fragment, appeared approximately 45 minutes into excystation and continued to be present throughout excystation. At the completion of excystation, the transcripts observed with the salinomycin-sensitive Guelph strain incubated in PBS were of higher molecular size (~1.35 and 1.15 kb) than when this strain was treated with salinomycin (~1.30 and 1.10 kb). The salinomycin-resistant strain incubated in PBS or treated with salinomycin each had two transcripts of approximately 1.30 and 1.10 kb. The expression rapidly declined in the salinomycin-resistant strain treated with salinomycin but the level of expression in the salinomycin-sensitive strain remained relatively constant.