A chromosomal t(11;18)(q21;q21) recurrently found in marginal zone lymphomas of mucosa-associated lymphocytic tissue (MALT) type is one of the key determinants of their treatment and outcome because t(11;18)-positive cases are resistant to Helicobacter pylori eradication therapy. To detect t(11;18) on paraffin-embedded tissue sections, we established a method of dual-color fluorescence in situ hybridization (D-FISH) using DNA probes directly labeled with SpectrumGreen and SpectrumOrange (tissue-FISH [T-FISH]). T-FISH detected the t(11;18) as colocalized signals between the band-specific yeast artificial chromosome (YAC) clones y966e4 (11q21) and y943b8 (18q21) on the der(11)t(11;18). The t(11;18) was detected in four of 22 patients with marginal zone lymphoma of MALT type in 72%-78% of the cells. In both patients studied, the percentage of t(11;18)-positive cells was much higher in tissue-FISH analysis than in interphase-FISH: 74% versus 30% in patient 1 and 75% versus 31% in patient 4. None of the 12 patients with diffuse large B-cell lymphoma of the stomach showed the t(11;18). Tissue-FISH is a powerful tool for the diagnosis of marginal zone lymphoma of MALT type because it can be applied not only to small specimens obtained from endoscopic biopsy samples but also to archival materials, hence facilitating the delineation of subtypes in marginal zone lymphoma of MALT type.