diff --git a/.appveyor.yml b/.appveyor.yml
index 9720dc2d..ca4d5049 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -7,6 +7,7 @@ version: 'vers.{build}'
 branches:
     except:
       - gh-pages
+      - /.*/ # Appveyor builds are currently disabled.
 
 # Do not build on tags (GitHub and BitBucket)
 skip_tags: true
diff --git a/.ci_helpers/clone b/.ci_helpers/clone
index c0b7c4d9..34054b86 100755
--- a/.ci_helpers/clone
+++ b/.ci_helpers/clone
@@ -18,7 +18,7 @@ ref=''
 [ -z "$ref" ] && repository='https://github.com/samtools/htslib.git'
 
 set -x
-git clone --recurse-submodules --shallow-submodules --depth=1 ${ref:+--branch="$branch"} "$repository" "$localdir"
+git clone --recurse-submodules --shallow-submodules --depth=2 ${ref:+--branch="$branch"} "$repository" "$localdir"
 
 # NB: "samtools" as the owner/organisation, not the repo name
 if [ "x$owner" = "xsamtools" -a -z "$ref" -a "x$htslib_PR" != "x" ]
diff --git a/.gitattributes b/.gitattributes
index 9d42c7c4..d765010a 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -10,3 +10,9 @@
 .git*           export-ignore
 .ci_helpers     export-ignore
 README.md       export-ignore
+
+# Prevent Windows cr-lf endings.
+test/**        -text
+test/**.c       text
+test/**.h       text
+test/**.pl      text
diff --git a/.github/workflows/windows-build.yml b/.github/workflows/windows-build.yml
new file mode 100644
index 00000000..49a14f37
--- /dev/null
+++ b/.github/workflows/windows-build.yml
@@ -0,0 +1,52 @@
+name: Windows/MinGW-W64 CI
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: windows-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+    - name: Set up MSYS2 MinGW-W64
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: mingw64
+        update: false
+        install: >-
+          mingw-w64-x86_64-toolchain
+          mingw-w64-x86_64-autotools
+          mingw-w64-x86_64-curl
+          mingw-w64-x86_64-libdeflate
+          mingw-w64-x86_64-tools-git
+          mingw-w64-x86_64-zlib
+          mingw-w64-x86_64-bzip2
+          mingw-w64-x86_64-xz
+    - name: Clone htslib
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+        .ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib htslib ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+        pushd .
+        cd htslib
+        autoreconf -i
+        popd
+    - name: Compile bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        autoheader
+        autoconf -Wno-syntax
+        ./configure --enable-werror
+        make -j4
+    - name: Check bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        make check
+