OBJECTIVE: Structured illumination microscopy is an inexpensive alternative to confocal microscopy that allows optical sectioning at a sub-cellular resolution. However, its application in imaging biological tissue has been limited by inadequate contrast present in them especially in reflectance imaging. Novel, optically active contrast agents like gold nanoparticles and quantum dots targeted against biomarkers of cancer can be integrated with structured illumination to image both the morphological and biochemical changes associated with epithelial pre-cancers. METHODS: We modified the optical path of a widefield microscope to implement structured illumination both in reflectance and fluorescence modes. For imaging, we used 25-nm-diameter gold nanoparticles and CdSe quantum dots for reflectance and fluorescence imaging, respectively, to label three-dimensional tissue constructs of SiHa cervical cancer cells. Contrast agents were targeted against the epidermal growth factor receptor (EGFR) using an anti-EGFR monoclonal antibody. Agents targeted with a non-specific IgG antibody served as a control to monitor non-specific labeling. RESULTS: Our result shows that optically sectioned images taken with structured illumination are very comparable to those obtained using confocal microscopy. Moreover, images of three-dimensional cultures stained with the anti-EGFR agents show significantly more image intensity than those stained with the IgG targeted control. CONCLUSION: Our findings suggest that the combination of novel optical contrast agents and structured illumination can differentiate neoplastic cells which overexpress EGFR from normal cells in intact tissue. Combining structured illumination microscopy with novel contrast agents can potentially provide a powerful and inexpensive tool to aid in the detection of cervical pre-cancers.