Mammalian cortical neurons integrate sensory information that arrives through numerous synaptic inputs located on their dendrites. Here we introduce an approach to identify sensory-evoked dendritic input sites in cortical neurons in vivo involving the use of two-photon calcium imaging combined with targeted whole-cell recordings. We provide basic technical descriptions as well as experimental procedures of this method. First, we discuss various scanning modes for two-photon imaging of cortical neuron dendrites in vivo. Second, we focus on practical aspects of dye-loading by means of whole-cell recordings in vivo. Third, we provide a step-by-step experimental protocol and a data analysis algorithm for dendritic imaging in cortical neurons. Fourth, we show, as an example, results obtained from dendrites of orientation-tuned neurons in layer 2/3 of mouse visual cortex. We conclude that the combination of whole-cell recording and two-photon calcium imaging is a useful tool for the functional mapping of input sites in dendrites that can be readily applied to other cortical areas and layers, helping to reveal the fine organization of sensory information representation in the dendrites of mammalian cortical neurons in vivo.