The objective of the present study was, due to increasing interest in the epidemiological role of small mammals as potential reservoir of Neospora caninum, to compare two different PCR protocols for the diagnosis of N. caninum in rodents. We tested tissue samples from 50 house mice (Mus musculus), 50 rats (Rattus norvegicus) and 35 field mice (Apodemus sylvaticus). Two different PCR protocols based on primer pairs, Np4-Np7 and Np6plus-Np21plus, were used for diagnosis on these samples. While there were not mismatches between the results of both PCR from rats or field mice, 49 out of 50 samples from house mice gave positive results with Np4-Np7 primer set. However after cloning and sequencing the PCR products, only six of these were confirmed to be N. caninum, while all the other 43 amplicons matched with house mice DNA sequence from clone RP23-14F5 on chromosome 11 sequence. Our results evidence that Np4-Np7 PCR could not be reliable in diagnosis of N. caninum in rodents.