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I've been trying to setup Cygwin to connect to github, but I've been having some issues. I'm on Windows 8, and I know that there's a problem in Cygwin on Windows 8 with the user groups and whatnot. I'm pretty sure I've fixed that already though. At the very least, I can change the permissions for any file properly now. Anyways, this is the output I get from Cygwin

ssh -vT

OpenSSH_6.2p2, OpenSSL 1.0.1e 11 Feb 2013
debug1: Connecting to [] port 22.
debug1: Connection established.
debug1: identity file /.ssh/id_rsa type 1
debug1: identity file /.ssh/id_rsa-cert type -1
debug1: identity file /.ssh/id_dsa type -1
debug1: identity file /.ssh/id_dsa-cert type -1
debug1: identity file /.ssh/id_ecdsa type -1
debug1: identity file /.ssh/id_ecdsa-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_6.2
debug1: Remote protocol version 2.0, remote software version OpenSSH_5.5p1 Debian-6+squeeze1+github12
debug1: match: OpenSSH_5.5p1 Debian-6+squeeze1+github12 pat OpenSSH_5*
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: server->client aes128-ctr hmac-md5 none
debug1: kex: client->server aes128-ctr hmac-md5 none
debug1: SSH2_MSG_KEX_DH_GEX_REQUEST(1024<1024<8192) sent
debug1: expecting SSH2_MSG_KEX_DH_GEX_GROUP
debug1: SSH2_MSG_KEX_DH_GEX_INIT sent
debug1: expecting SSH2_MSG_KEX_DH_GEX_REPLY
debug1: Server host key: RSA 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48
debug1: Host '' is known and matches the RSA host key.
debug1: Found key in /.ssh/known_hosts:1
debug1: ssh_rsa_verify: signature correct
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: Roaming not allowed by server
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey
debug1: Next authentication method: publickey
debug1: Offering RSA public key: /.ssh/id_rsa
debug1: Authentications that can continue: publickey
debug1: Trying private key: /.ssh/id_dsa
debug1: Trying private key: /.ssh/id_ecdsa
debug1: No more authentication methods to try.
Permission denied (publickey).

Something interesting when I run this:

$ ssh-add -l
Could not open a connection to your authentication agent.

I'll also point out that I can use git just fine on Powershell.

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Does the output of ssh-keygen -lf ~/.ssh/ match the key signature in github? source – Justin Wrobel Aug 1 '13 at 15:32
up vote 0 down vote accepted

It maybe that your ssh-agent is started from your PowerShell startup files. That's probably why it works there.

The simpler fix is to start another agent. You can use PuTTY's Pageant. Check here how to configure your shell to setup connection to Pageant so that ssh-add and ssh will use it:

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