diff --git a/.appveyor.yml b/.appveyor.yml
deleted file mode 100644
index 9720dc2dd..000000000
--- a/.appveyor.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-# version format.
-# you can use {branch} name in version format too
-# version: 1.0.{build}-{branch}
-version: 'vers.{build}'
-
-# branches to build
-branches:
-    except:
-      - gh-pages
-
-# Do not build on tags (GitHub and BitBucket)
-skip_tags: true
-
-# Skipping commits affecting specific files (GitHub only). More details here: /docs/appveyor-yml
-#skip_commits:
-#  files:
-#    - docs/*
-#    - '**/*.html'
-
-# Appveyor Windows images are based on Visual studio version
-image: Visual Studio 2019
-
-# We use Mingw/Msys, so use pacman for installs
-install:
-  - set HOME=.
-  - set MSYSTEM=MINGW64
-  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
-  - set MINGWPREFIX=x86_64-w64-mingw32
-  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-autotools mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\""
-
-# The user may have e.g. jkbonfield/bcftools branch FOO and an associated
-# jkbonfield/htslib branch FOO.  If so use that related htslib, obtained by
-# munging $APPVEYOR_REPO_NAME.  Otherwise we assume this is a PR only to
-# bcftools and should be linked against samtools(org)/htslib develop branch.
-clone_script:
-  - "sh -lc \"if test x$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME != x ; then git clone --branch=$APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH https://github.com/$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME $APPVEYOR_BUILD_FOLDER ; else false ; fi || git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/$APPVEYOR_REPO_NAME $APPVEYOR_BUILD_FOLDER\""
-  - "sh -lc \"git show-branch --sha1-name HEAD"
-  - "sh -lc \"git clone --recurse-submodules --shallow-submodules --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/bcftools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone --recurse-submodules --shallow-submodules https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \""
-  - "sh -lc \"cd $APPVEYOR_BUILD_FOLDER/htslib && git show-branch --sha1-name HEAD\""
-
-build_script:
-  - set HOME=.
-  - set MSYSTEM=MINGW64
-  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
-  - "sh -lc \"(cd htslib; autoreconf -i)\""
-  - "sh -lc \"autoreconf -i && ./configure --enable-werror && make -j2\""
-
-test_script:
-  - set HOME=.
-  - set MSYSTEM=MINGW64
-  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%APPVEYOR_BUILD_FOLDER%/htslib;%PATH%
-  - "sh -lc \"MSYS2_ARG_CONV_EXCL=* make test-plugins\""
diff --git a/.ci_helpers/clone b/.ci_helpers/clone
index c0b7c4d95..34054b863 100755
--- a/.ci_helpers/clone
+++ b/.ci_helpers/clone
@@ -18,7 +18,7 @@ ref=''
 [ -z "$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 9d42c7c43..8c3a1419d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -10,3 +10,6 @@
 .git*           export-ignore
 .ci_helpers     export-ignore
 README.md       export-ignore
+
+# Prevent Windows cr-lf endings.
+test/**        -text
diff --git a/.github/workflows/windows-build.yml b/.github/workflows/windows-build.yml
new file mode 100644
index 000000000..49a14f37f
--- /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
+