A near-infrared Raman spectroscopy system integrated with multimodal endoscopic imaging has been developed for in vivo diagnosis and detection of gastric malignancies during clinical gastroscopic examinations. In this study, 1238 high-quality in vivo Raman spectra in the range 800-1800 cm-1 were acquired from gastric normal and malignant tissue within 0.5 second from 81 patients under the guidance of white-light (WL), narrow-band (NB) and autofluorescence (AF) imaging during clinical endoscopy. Significant differences in Raman spectral shapes and intensities between normal and malignant gastric mucosal tissue were observed, particularly in the spectral ranges 800-900, 1000-1100, 1250-1450 and 1600-1800 cm-1, which primarily contain signals related to proteins, nucleic acids and lipids. Partial least squares discriminant analysis (PLS-DA) could identify in vivo Raman spectra of neoplasia with a sensitivity of 82.9% and specificity of 88.9% using leave-one-tissue site out cross validation. This study demonstrates that in vivo Raman spectroscopy in conjunction with multimodal endoscopic imaging modalities holds a great promise for improving the early diagnosis of gastric malignancies.© (2010) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.