In vivo studies of neurophysiology using the whole-cell patch clamp technique enable exquisite access to both intracellular dynamics and cytosol of cells in the living brain but are underrepresented in deep subcortical nuclei due to fouling of the sensitive electrode tip. We have developed an autonomous method to navigate electrodes around obstacles such as blood vessels, after identifying them as a source of contamination during regional pipette localization (RPL) in vivo. In mice, robotic navigation prevented fouling of the electrode tip, increasing RPL success probability 3 mm below the pial surface to 82% (n=72/88) over traditional, linear localization (25%, n=24/95) and resulted in high quality thalamic whole-cell recordings with average access resistance (32.0 MO), and resting membrane potential (-62.9 mV) similar to cortical recordings in isoflurane-anesthetized mice. Whole-cell yield improved from 1% (n=1/95) to 10% (n=9/88) when robotic navigation was used during RPL. This method opens the door to whole-cell studies in deep subcortical nuclei, including multimodal cell typing and studies of long range circuits.