Many techniques have been proposed to divide the brain based on structural connectivity. However, even when produced by the same technique, the resulting parcellations tend to differ in the number, shape, and spatial localization of parcels across subject. Matching parcels across subjects is an open problem. We propose to use Optimal Transport (OT) theory to tackle this issue. OT theory studies the efficient transportation of mass between two probability distributions with respect to a certain cost function. As a proof of concept, we show that OT can match parcels of the Desikan atlas across different subjects, using only the structural connectivity fingerprint of each parcel. We use the Desikan atlas since it is used as a prior parcellation in several connectivity studies. For comparison purposes we also match parcels using two additional methods based on the Euclidean and cosine distance. Our results show that the technique based on OT is the most efficient.