Dry eye disease (DED) is one of the most common ocular disorders worldwide. The pathophysiological mechanisms involved in the development of DED are not well understood and thus treating DED has been a significant challenge for ophthalmologists. Most of the currently available diagnostic tests demonstrate low correlation to patient symptoms and have low reproducibility. Recently, sophisticated in vivo imaging modalities have become available for patient care, namely, in vivo confocal microscopy (IVCM) and optical coherence tomography (OCT). These emerging modalities are powerful and non-invasive, allowing real-time visualization of cellular and anatomical structures of the cornea and ocular surface. Here we discuss how, by providing both qualitative and quantitative assessment, these techniques can be used to demonstrate early subclinical disease, grade layer-by-layer severity, and allow monitoring of disease severity by cellular alterations. Imaging-guided stratification of patients may also be possible in conjunction with clinical examination methods. Visualization of subclinical changes and stratification of patients in vivo, allows objective image-guided evaluation of tailored treatment response based on cellular morphological alterations specific to each patient. This image-guided approach to DED may ultimately improve patient outcomes and allow studying the efficacy of novel therapies in clinical trials.