A fluorescence-based technique was established to trace intracellular sporozoites of Eimeria bovis for tests on gliding motility, invasion, replication and quantification of infection rates in cultured bovine umbilical vein endothelial cells (BUVEC) by laser scanning confocal microscopy and flow cytometry (FCM) analyses. Employing the fluorescent dye 5(6)-carboxyfluorescein diacetate succinimidyl ester (CFSE), we determined its effects on sporozoites at various concentrations and duration of staining. More than 98% of sporozoites were labelled with the dye at a concentration of 2.5 muM. Staining was predominantly found in refractile bodies and presumptive micronemes. Upon infection of BUVEC, CFSE-labelled sporozoites developed into fluorescent immature macromeronts, which were traceable inside the cells until 22 days postinfection (p. i.). Consistent with a peripheral localisation of the fluorescence signal in macromeronts merozoites released from these lacked detectable fluorescence. As example of use, a multicolour FCM approach for the simultaneous determination of E. bovis infection and host cell surface molecule expression was established. The approach proved suitable to quantify major histocompatibility complex (MHC-I) and MHC-II expression, thereby clearly distinguishing between infected and uninfected BUVEC up to day 14 p. i. In conclusion, CFSE labelling of E. bovis sporozoites facilitates monitoring of intracellular stages in vitro and will be a highly useful tool for studying host cell responses towards parasite invasion.