A fluorescence confocal microscopy technique was employed to obtain subsurface images of nerve and microvascular structure in the vas deferens and colon of the living rat. The use of dual labelling with vital dyes and 2-channel confocal acquisition allowed differentiation of microscopic structure at both low and higher magnification. Characteristic staining patterns of nerves and blood vessels were repeatedly obtained in each tissue, suggesting the potential of this technique for studying morphological changes associated with surgical procedures and/or models of neuronal or vascular pathology.