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Quantum key distribution (QKD) provides ultimate cryptographic security based on the laws of quantum mechanics. For point-to-point QKD protocols, the security of the generated key is compromised by detector side channel attacks. This problem can be solved with measurement-device-independent QKD (mdi-QKD). However, mdi-QKD has shown limited performances in terms of the secret key generation rate, due to postselection in the Bell measurements. We show that high-dimensional (Hi-D) encoding (qudits) improves the performance of current mdi-QKD implementations. The scheme is proven to be unconditionally secure even for weak coherent pulses with decoy states, while the secret key rate is derived in the single-photon case. Our analysis includes phase errors, imperfect sources, and dark counts to mimic real systems. Compared to the standard bidimensional case, we show an improvement in the key generation rate.