Raman spectroscopy is a non-invasive optical technique capable of measuring vibrational modes of biomolecules within viable tissues. In this study, we evaluated the application of an integrated real-time system of Raman spectroscopy for in vivo skin cancer diagnosis. Benign and malignant skin lesions (n=518) from 453 patients were measured within one second, including melanomas, basal cell carcinomas, squamous cell carcinomas, actinic keratoses, atypical nevi, melanocytic nevi, blue nevi and seborrheic keratoses. Lesion classification was made using principal component with general discriminant analysis and partial least squares, in three distinct discrimination tasks: skin cancers and precancers from benign skin lesions (ROC=0.879); melanomas from non-melanoma pigmented lesions (ROC=0.823); and melanomas from seborrheic keratoses (ROC=0.898). For sensitivities between 95- 99%, the specificities ranged between 15-54%. Our findings establish that real-time Raman spectroscopy can be used distinguish malignant from benign skin lesions with good diagnostic accuracy comparable to clinical examination and other optical-based methods.