After high school, Rothlin chose to major in biochemistry for her undergraduate degree at the University of Buenos Aires. Rothlin stayed at the University of Buenos Aires for her graduate degree in biochemistry. She was mentored by Ana Belén Elgoyhen and studied the biochemical properties of the nicotinic acetylcholine receptors in the inner ear. Her work helped further our understanding of how efferent cholinergic fibers and inner ear hair cells communicate to relay information from the brain back to the ear to mediate sensory tuning.
