Edit the root commit in Git?

Assuming that you have a clean working tree, you can do the following.

# checkout the root commit
git checkout <sha1-of-root>

# amend the commit
git commit --amend

# rebase all the other commits in master onto the amended root
git rebase --onto HEAD HEAD master

To expand on ecdpalma's answer, you can now use the --root option to tell rebase that you want to rewrite the root/first commit:

git rebase --interactive --root

Then the root commit will show up in the rebase TODO list, and you can select to edit or reword it:

reword <root commit sha> <original message>
pick <other commit sha> <message>
...

This is the explanation of --root from the Git rebase docs (emphasis mine):

Rebase all commits reachable from <branch>, instead of limiting them with an <upstream>. This allows you to rebase the root commit(s) on a branch.

As of Git version 1.7.12, you may now use

git rebase -i --root

Documentation

Just to provide an alternative to the higher rated answers:

If you are creating a repo, and know upfront that you'll be rebasing on top of its "first" real commit in the future, you can avoid this problem altogether by making an explicit empty commit at the beginning:

git commit --allow-empty -m "Initial commit"

and only then start doing "real" commits. Then you can easily rebase on top of that commit the standard way, for example git rebase -i HEAD^