Background Endoscopic brush cytology is a promising surveillance technique for Barrett’s esophagus. However, there is a need for ancillary biomarkers to incr ease the sensitivity of cytology and to allow identification of patients at increased risk for disease progression. The aims of this study were to eval uate the feasibility of fluorescence in situ hybridization of endoscopic brush c ytology specimens and to determine if there are specific chromosomal changes in cytologic specimens from patients with cancer that are not present in patients w ithout dysplasia. Methods Archival cytology slides from 16 patients with Barrett ’s esophagus were studied: 8 negative for dysplasia and 8 positive for adenocar cinoma. Fluorescence in situ hybridization was used to detect two alterations: H ER-2 gene(17q11.2-q12) and 20q13.2 region amplification. Observations For 7 of 8 adenocarcinoma cases, there was amplification/aneusomy of at least one of the two analyzed regions by fluorescence in situ hybridization. None of the samples negative for dysplasia were abnormal for either of the two genomic regions stud ied.Conclusions Fluorescence in situ hybridization is feasible by using routine Barrett’s esophagus cytologic specimens. Differences in genomic makeup can be d etected in cells from patients negative for dysplasia and in those with adenocar cinoma. Background Endoscopic brush cytology is a promising surveillance technique for Barrett’s esophagus. However, there is a need for ancillary biomarkers to incr ease the sensitivity of cytology and to allow identification of patients at increased risk for disease progression. The aims of this study were to eval uate the feasibility of fluorescence in situ hybridization of endoscopic brush c ytology specimens and determine if there are specific chromosomal changes in cytologic specimens from patients with cancer that are not present in patients w ithout dysplasia. Methods Archival cytology slides from 16 patients with Barrett ’ 7 esophagus were studied: 8 negative for dysplasia and 8 positive for adenocar cinoma. Fluorescence in situ hybridization was used to detect two alterations: H ER-2 gene (17q11.2-q12) and 20q13.2 region amplification. Observations For 7 of 8 adenocarcinoma cases, there was amplification / aneusomy of at least one of the two rainfall regions by fluorescence in situ hy None of the samples negative for dysplasia were abnormal for either of the two genomic regions studied. Conclusions Fluorescence in situ hybridization is feasible by using routine Barrett’s esophagus cytologic specimens. Differences in genomic makeup can be d etected in cells from patients negative for dysplasia and in those with adenocar cinoma.