Addition of an extra methionine at the N-terminus by recombinant expression of α-lactalbumin in Escherichia coli significantly destabilizes the protein, and this destabilization has hampered mutational analyses such as the mutational phi-value analysis of the protein. Deletion of residue 1 from the recombinant form recovers the stability in human and goat α-lactalbumin. Here, we thus determined the crystal structures of the residue 1-deletion variants of recombinant human and goat α-lactalbumin, and compared the structures with those of the authentic and recombinant forms. The results demonstrate the importance of the N-terminal backbone structure and hydrogen-bonding pattern for the stability of α-lactalbumin.