Standardisation and unification of diagnostic methods and their improvement were the first emerging problems when seed pathologists of different laboratories and countries compared their own data. Classic methodologies have been focused on fungi detection, principally by means of incubation and grow-out methods. Despite their utility, traditional methods are often time and space consuming and sometimes they are not enough sensible to low levels of seed infection. In the 1980's new diagnostic technologies (i.e., ELISA, ISEM, etc.) were successfully applied to the seed and they resulted very sensitive for the detection of viruses, bacteria and fungi at very low infection levels in the seed. Recently, new emerging techniques based on DNA analysis (e.g. polymerase chain reaction, PCR) resulted very efficient in diagnosis since they have high sensitivity and specificity. Despite their advantages, DNA analysis results must be correctly interpreted because they do not distinguish between vital and non-vital inoculum and there are no indications on the exact location of the inoculum in the seed. Other problem could be the occurrence of false negative or false positive results. However, before the application of the innovative molecular techniques on a large scale, it is necessary to compare the results obtained on the sub-samples in different laboratories.