Seven laboratories decided to compare their molecular diagnostic techniques to identify Mediterranean theileriosis caused by Theileria annulata. Each laboratory used either PCR or PCR and reverse line blot hybridization (RLB) to identify T. annulata. Five laboratories sent their own samples to laboratory 4 to be recoded and passed on to at least two other laboratories. A total of 120 blood samples were analyzed during this study, generating 540 results. Laboratory 1 sent only T. annulata-infected samples (positive control batch), and all the laboratories testing this batch found 100% infection. Laboratory 2 sent only negative samples from a Mediterranean area where T. annulata was unknown, and two laboratories out of three found a few positive samples in these negative samples. For the remaining samples, detection performance was variable. Agreement between laboratories ranged from 21.4 to 91.3%. The overall mismatch between laboratories was around 30% by whatever technique used. This paper describes the methodological parameters that could explain the variation of results.