In both stories, the protagonists—Aylmer in "The Birthmark" and the titular Goodman Brown—use their wives, Georgiana and Faith, respectively, in order to better their own situations.

Regarding the removal of her birthmark, Aylmer says to his wife, "'what will be my triumph when I shall have corrected what Nature left imperfect in her fairest work!'" He feels absolutely assured of his ability to succeed in removing the crimson hand that marks her cheek, the birthmark that he feels is the only thing to mar her otherwise perfect beauty. Aylmer believes that, when he succeeds in perfecting what nature could not, he will have achieved the ultimate triumph. It is his pride which matters to him, not her feelings or her life. In rendering her face without flaw, he will gratify himself and his own arrogant pride.

As Goodman Brown heads out into the forest to meet with the Devil, he regrets causing his wife any concern. She does not want him to leave her, but he insists that he must go. He thinks to himself:

Well; she's a blessed angel on earth; and after this one night, I'll cling to her skirts and follow her to Heaven.

In other words, Brown plans to rely on Faith's good works and morality in order to get into heaven. He does not want to have to do the hard work himself, and so he will merely follow her example after this. He thinks that he will gain easy passage to heaven by following her.

Thus, neither Aylmer nor Goodman Brown seems to truly love or care about his wife as a person. Georgiana is to be an experiment to gratify her husband's pride, and Faith is to be a model to smooth her husband's passage to heaven. Neither woman is loved for who she is, but only really what she can do for her husband.

Further, it is notable that neither man is successful in his endeavor to use his wife in this way: Aylmer does rid Georgiana of her birthmark, but he kills her in the process—no human being can be perfect; to be human is to be flawed. Brown cannot follow Faith to heaven because he loses his own Christian faith when he goes to the woods. In the forest, he learned that we are all imperfect sinners and inherently flawed.

Both stories by Nathaniel Hawthorne feature his signature dark outlook on humanity.  In "Young Goodman Brown" the titular character, though a Puritan, does not fully surrender to the teachings of his faith and must witness for himself the temptations of the devil. As a result of his nocturnal foray into the forest, he loses his faith in both his fellow man and his religion. Hawthorne seems to suggest that to look too deeply into one's faith may not offer the security one expects—and that man might be inherently evil.

"The Birthmark" is similar in that Hawthorne offers a dark outlook on humanity. Aylmer does not accept Georgiana's "imperfection" and believes that he alone can "perfect" her beauty by removing her birthmark. Aylmer believes he possesses abilities beyond what most people possess, and he feels compelled to put it to an extreme test.  Like Goodman Brown, Aylmer's "test" results in tragedy.

Thematically, the stories are similar in that both men consider themselves somehow more capable than others, they believe they possess more courage, skill, or knowledge, and they are brought down by their excessive pride.

The stories differ in their approach to how the protagonist is brought down.  "Young Goodman Brown" uses the vehicle of faith as the means to the protagonist's downfall, while "The Birthmark" uses the vehicle of imperfectly understood science as the agent of the protagonist's destruction.

The main similarity between the two stories is the idealistic protagonists in each.  In The Birthmark, Aylmer arrogantly believes that he has the skill to perfect in his wife what nature had left imperfect.  His idealistic dreams lead to a tragic end, however, when the potion he gives his wife removes her one earthly imperfection, making it impossible for her to remain on earth any longer.

In Young Goodman Brown, the protagonist has an idealistic view of his religious faith and those who have instructed him in that faith.  He arrogantly meets with the devil in the woods at night, thinking that he is strong enough to toy with evil and walk away unharmed.  When he sees distinguished members of his church congregation heading toward the evil assembly, his faith is shattered.  Like Aylmer, his idealistic pride led to a tragic end.

The most significant difference between the two stories is one emphasizes science and the other religion (or faith).  The Birthmark deals with science as it was understood during Hawthorne's time period.  Young Goodman Brown is set during the Puritan time period and focuses on their strict religious faith.