I have Cygwin installed on Windows 7. I made default install. I would like to use ssh config file (~/.ssh/config) to set host and options for connecting.

Normal ssh command is not able to find the config while I try to connect: ssh host If I explicitly specify config file, everything is OK: ssh -F ~/.ssh/config

I cannot found any option to set ssh client, something like /etc/ssh

Maybe ssh doesn't know where is my home folder? (I have set HOME environment variable to my home folder)


Install the openssh package and then run ssh-host-config. It will generate a "ssh_config" file in /etc/.


I had the same issue. I wanted to use ~/.ssh/config because I was already using that directory for other applications and didn't want to maintain 2 copies. So creating an /etc/ssh_config directory wasn't the ideal solution.

As Fujimoto Youichi mentions, ssh looks at /etc/passwd for your home directory and not the $HOME environment variable.

The current cygwin versions (I'm using 2.6) no longer creates /etc/passwd as part of the install. However, it is easy to create a new one:

    mkpasswd -c -p "$(cygpath -H)" > /etc/passwd
  • -c Adds the current user to the passwd file
  • -p "$(cygpath -H)" Adds your current home directory

https://cygwin.com/cygwin-ug-net/mkpasswd.html has more details on the available flags.

I haven't looked at the code, but ssh's preference seems to be:

  1. /etc/ssh_config
  2. ~/.ssh/config

So if you only want to use the ssh configuration information from ~/.ssh/config, then be sure to delete /etc/ssh_config.

Also, be sure to open a new cygwin terminal window after making changes, for them to become available.

  • seems it's been relocated to /etc/defaults/ssh_config – VeraKozya Feb 4 '19 at 19:40

ssh command looks for its config file under home directory from /etc/passwd. So setting HOME variable will not work.

There are many ways but we can fix it by simply making a symlink as follows.

ln -s ~ /home


The other answers didn't work for me. I just created c:\cygwin64\etc\ssh_config and pasted in the following default / example file:

# This is the ssh client system-wide configuration file.  See
# ssh_config(5) for more information.  This file provides defaults for
# users, and the values can be changed in per-user configuration files
# or on the command line.

# Configuration data is parsed as follows:
#  1. command line options
#  2. user-specific file
#  3. system-wide file
# Any configuration value is only changed the first time it is set.
# Thus, host-specific definitions should be at the beginning of the
# configuration file, and defaults at the end.

# Site-wide defaults for some commonly used options.  For a comprehensive
# list of available options, their meanings and defaults, please see the
# ssh_config(5) man page.

# Host *
#   ForwardAgent no
#   ForwardX11 no
#   RhostsRSAAuthentication no
#   RSAAuthentication yes
#   PasswordAuthentication yes
#   HostbasedAuthentication no
#   GSSAPIAuthentication no
#   GSSAPIDelegateCredentials no
#   BatchMode no
#   CheckHostIP yes
#   AddressFamily any
#   ConnectTimeout 0
#   StrictHostKeyChecking ask
#   IdentityFile ~/.ssh/identity
#   IdentityFile ~/.ssh/id_rsa
#   IdentityFile ~/.ssh/id_dsa
#   Port 22
#   Protocol 2,1
#   Cipher 3des
#   Ciphers aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-cbc,3des-cbc
#   MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160
#   EscapeChar ~
#   Tunnel no
#   TunnelDevice any:any
#   PermitLocalCommand no
#   VisualHostKey no
#   ProxyCommand ssh -q -W %h:%p gateway.example.com
Host *
    Port 22

Hope that helps the next person.


According to the accepted answer, by use command to initialize:


You can also create empty /etc/ssh_config in Cygwin, which will work same.

The /etc/ssh_config creating by ssh-host-config is also empty with all comment out lines.

Reload SSH with new config:

To effect config, you can just finish editing /etc/ssh_config without restart service.

  • 1
    How does this differ from the accepted answer? – Greenonline Jun 15 '17 at 4:05
  • I can not comment on it to further explain the principle and how to effect the ssh config. – Nick Tsai Jun 15 '17 at 5:27
  • You need to earn some reputation first. Try editing some badly formatted posts, or answering an unanswered question :-) – Greenonline Jun 15 '17 at 5:28
  • OK! I posted this answer because after checking the accepted answer, I did more survey on it. Thank you. – Nick Tsai Jun 15 '17 at 5:32

Cygwin ssh expects the config to be in /home/$USER. But the home directory "~" in cygwin is C:/Users/$USER, indeed /home is empty. You can have both C:/Users/$USER/.ssh and /home/$USER/.ssh be valid paths, by creating a symlink:

ln -s ~ /home/$USER

The currently accepted answer did not fix the problem for me. Instead I symlinked the .ssh directory from my Windows user account's home directory into my Cygwin user's home directory:

ln -s /cygdrive/c/Users/<MY-USER>/.ssh /home/<MY-USER>/.ssh

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.