Citrus tristeza virus (CTV) is the causing agent of an economically significant citrus fruit disease. Depending on the combination of hosts/genotypes of the virus, the intensity of the symptoms may vary. Among strong symptoms is the stem pitting, characterized by a deformation of the wood of the infected plant characterized by the occurrence of small holes/pits. The goal of the work was to use the ELISA method to search for the presence of the CTV virus in 46 indicator plants, which were experimentaly infected in 2008, and to determine the possible differences in the “survival” of the different virus genotypes. Apart from the standard ELISA detection by using the phloem extracts, the characteristic tissue where virus replicates, detection of the virus from transverse cuts of the branches, with and without the phloem tissue was also conducted. The hypothesis was that the modified method when using the cuts with the phloem tissue will give results identical to those gained from the phloem extract, while using the branch cuts without the phloem will give positive results only in those plants in which the presense of stem pitting symptom has been observed. Using standard ELISA detection, the presence of the virus was confirmed in 52.2% of the samples, and a difference in the rate of “survival” of the different viral genotypes has been observed. The sensitivity of testing by the modified procedure using the wood with the phloem showed less sensitivity when compared with the standard ELISA protocol. The modified method using the cuts without the phloem confirmed the presence of the virus in 66,7% of samples related to stem pitting symptoms, which points to a prospective of a modified method in a selective detection of stem pitting causing viral genotypes.