diff --git a/.Rbuildignore b/.Rbuildignore
index 1d20737..a981b71 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,4 @@
 ^autom4te\.cache$
 ^config\.log$
 ^config\.status$
+^\.gitattributes$
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..c6bc410
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,6 @@
+# Ensure shell scripts and configure files always use LF line endings
+configure text eol=lf
+configure.ac text eol=lf
+configure.win text eol=lf
+cleanup text eol=lf
+*.sh text eol=lf
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2ff3f6f..980245d 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -18,12 +18,14 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
+          #- {os: macos-latest,   r: 'release'}
+          #- {os: ubuntu-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      INTEL_OPENCL_URL: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/b6dccdb7-b503-41ea-bd4b-a78e9c2d8dd6/w_opencl_runtime_p_2025.1.0.972.exe"
 
     steps:
       - uses: actions/checkout@v4
@@ -38,12 +40,80 @@ jobs:
 
       - name: Install clblast via Homebrew (macOS)
         if: runner.os == 'macOS'
-        run: brew install clblast clblas
+        run: brew install clblast clblas clinfo
 
       - name: Install clblast via apt (Ubuntu)
         if: runner.os == 'Linux'
         run: sudo apt-get update && sudo apt-get install -y opencl-headers ocl-icd-opencl-dev libclblast-dev
 
+      - name: Cache Intel OpenCL Runtime
+        if: runner.os == 'Windows'
+        id: cache-opencl-win
+        uses: actions/cache@v5
+        with:
+          # Default install location is x86 ... 
+          path: C:\Program Files (x86)\Common Files\Intel\Shared Libraries
+          key: intel-opencl-runtime-2025.3.1
+          
+      - name: Install OpenCL SDK (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          vcpkg install opencl:x64-windows clblast:x64-windows
+          # Convert to forward slashes to avoid escaping issues in configure.win
+          $vcpkgPath = "$env:VCPKG_INSTALLATION_ROOT/installed/x64-windows" -replace '\\','/'
+
+          # Register OpenCL location
+          echo "OPENCL_CPPFLAGS=-I$vcpkgPath/include" >> $env:GITHUB_ENV
+          echo "OPENCL_LIBS=-L$vcpkgPath/lib -lOpenCL" >> $env:GITHUB_ENV
+
+          # Register CLBlast location
+          echo "CLBLAST_CPPFLAGS=-I$vcpkgPath/include" >> $env:GITHUB_ENV
+          echo "CLBLAST_LIBS=-L$vcpkgPath/lib -lclblast" >> $env:GITHUB_ENV
+
+          # Add vcpkg bin to PATH so DLLs can be found at runtime
+          echo "$env:VCPKG_INSTALLATION_ROOT\installed\x64-windows\bin" >> $env:GITHUB_PATH
+          
+      - name: Install Intel CPU Runtime for OpenCL (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          # Download
+          curl -o opencl-installer.exe "${{ env.INTEL_OPENCL_URL }}"
+          
+          # Extract MSI from the self-extracting exe
+          $proc = Start-Process "./opencl-installer.exe" "-s -x -f extracted" -NoNewWindow -PassThru
+          $proc.WaitForExit()
+          
+          # Install via msiexec
+          $msi = Get-ChildItem ./extracted/*.msi | Select-Object -First 1
+          $proc = Start-Process "msiexec" "/i `"$msi`" /qn /l*! install.log" -NoNewWindow -PassThru
+          $proc.WaitForExit()
+          
+          if ($proc.ExitCode -ne 0) {
+            Get-Content install.log
+            exit $proc.ExitCode
+          }
+          
+          Remove-Item -Recurse -Force extracted, opencl-installer.exe
+      
+      - name: Register Intel OpenCL ICD (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $dllPath = "C:\Program Files (x86)\Common Files\Intel\Shared Libraries\bin\OpenCL.dll"
+          REG ADD "HKLM\SOFTWARE\Khronos\OpenCL\Vendors" /v $dllPath /t REG_DWORD /d 0 /f
+          REG ADD "HKLM\SOFTWARE\Wow6432Node\Khronos\OpenCL\Vendors" /v $dllPath /t REG_DWORD /d 0 /f
+          Add-Content $env:GITHUB_PATH "C:\Program Files (x86)\Common Files\Intel\Shared Libraries\bin\"
+
+      - name: Debug OpenCL paths
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          echo "OPENCL_CPPFLAGS: $env:OPENCL_CPPFLAGS"
+          echo "OPENCL_LIBS: $env:OPENCL_LIBS"
+          ls "$env:VCPKG_INSTALLATION_ROOT\installed\x64-windows\include\CL"
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
diff --git a/configure.win b/configure.win
new file mode 100755
index 0000000..63aa438
--- /dev/null
+++ b/configure.win
@@ -0,0 +1,184 @@
+#!/bin/sh
+##
+## RcppBandicoot configure.win
+##
+## Windows-specific configuration script
+## Detects OpenCL and CLBlast from environment variables
+##
+## Copyright (C) 2023-2025 James Balamuta
+## Licensed under GPL-2 or later
+##
+
+echo "Configuring RcppBandicoot for Windows..."
+
+## Get R_HOME
+: ${R_HOME=$(R RHOME)}
+if test -z "${R_HOME}"; then
+    echo "ERROR: Could not determine R_HOME"
+    exit 1
+fi
+
+## Default values
+BANDICOOT_CXXFLAGS=""
+BANDICOOT_LIBS=""
+OPENMP_CXXFLAGS='$(SHLIB_OPENMP_CXXFLAGS)'
+OPENCL_TARGET_VERSION=300
+
+## Kernel source directory (matches configure.ac logic)
+BANDICOOT_KERNELS_DIR=$("${R_HOME}/bin/Rscript" -e 'cat(paste(head(.libPaths(),1), "RcppBandicoot", "include", "bandicoot_bits", "ks", "", sep="/"))')
+
+## Always disable CUDA on Windows (requires manual setup)
+BANDICOOT_CXXFLAGS="${BANDICOOT_CXXFLAGS} -DCOOT_DONT_USE_CUDA"
+
+## Check for OpenCL headers via environment variable
+if [ -n "${OPENCL_CPPFLAGS}" ]; then
+    echo "  OpenCL headers: found (via OPENCL_CPPFLAGS)"
+    BANDICOOT_CXXFLAGS="${BANDICOOT_CXXFLAGS} -DCOOT_USE_OPENCL ${OPENCL_CPPFLAGS}"
+    HAVE_OPENCL=1
+else
+    echo "  OpenCL headers: not found"
+    echo "  Set OPENCL_CPPFLAGS to specify OpenCL header location"
+    HAVE_OPENCL=0
+fi
+
+## Check for OpenCL library
+if [ -n "${OPENCL_LIBS}" ]; then
+    echo "  OpenCL library: found (via OPENCL_LIBS): ${OPENCL_LIBS}"
+    BANDICOOT_LIBS="${BANDICOOT_LIBS} ${OPENCL_LIBS}"
+else
+    echo "  OpenCL library: not found (OPENCL_LIBS not set)"
+    echo "  WARNING: Linking will fail without OpenCL library!"
+fi
+
+## Check for CLBlast via environment variable
+if [ -n "${CLBLAST_CPPFLAGS}" ]; then
+    echo "  CLBlast: found (via CLBLAST_CPPFLAGS)"
+    BANDICOOT_CXXFLAGS="${BANDICOOT_CXXFLAGS} -DCOOT_USE_CLBLAST ${CLBLAST_CPPFLAGS}"
+    HAVE_CLBLAST=1
+else
+    echo "  CLBlast: not found, disabling"
+    BANDICOOT_CXXFLAGS="${BANDICOOT_CXXFLAGS} -DCOOT_DONT_USE_CLBLAST"
+    HAVE_CLBLAST=0
+fi
+
+## Check for CLBlast library
+if [ -n "${CLBLAST_LIBS}" ]; then
+    echo "  CLBlast library: ${CLBLAST_LIBS}"
+    BANDICOOT_LIBS="${BANDICOOT_LIBS} ${CLBLAST_LIBS}"
+fi
+
+## Always disable clBLAS (CLBlast is preferred)
+BANDICOOT_CXXFLAGS="${BANDICOOT_CXXFLAGS} -DCOOT_DONT_USE_CLBLAS"
+HAVE_CLBLAS=0
+
+## Add common flags
+BANDICOOT_CXXFLAGS="${OPENMP_CXXFLAGS} ${BANDICOOT_CXXFLAGS}"
+
+## Add R's LAPACK/BLAS
+BANDICOOT_LIBS="${BANDICOOT_LIBS} \$(LAPACK_LIBS) \$(BLAS_LIBS) \$(FLIBS)"
+
+## Check if we have at least OpenCL
+if [ "${HAVE_OPENCL}" = "0" ]; then
+    echo ""
+    echo "WARNING: No GPU backend detected!"
+    echo ""
+    echo "RcppBandicoot requires OpenCL headers to compile on Windows."
+    echo "Set the following environment variables before building:"
+    echo ""
+    echo "  OPENCL_CPPFLAGS  - Path to OpenCL headers (e.g., -IC:/OpenCL/include)"
+    echo "  OPENCL_LIBS      - OpenCL library flags (e.g., -LC:/OpenCL/lib -lOpenCL)"
+    echo "  CLBLAST_CPPFLAGS - Path to CLBlast headers (optional)"
+    echo "  CLBLAST_LIBS     - CLBlast library flags (optional)"
+    echo ""
+fi
+
+echo ""
+echo "Configuration Summary:"
+echo "  OpenCL:  ${HAVE_OPENCL}"
+echo "  CLBlast: ${HAVE_CLBLAST}"
+echo "  CUDA:    disabled (Windows)"
+echo "  Kernels: ${BANDICOOT_KERNELS_DIR}"
+echo ""
+
+## Generate Makevars.win from template
+if [ -f "src/Makevars.win.in" ]; then
+    sed -e "s|@BANDICOOT_CXXFLAGS@|${BANDICOOT_CXXFLAGS}|g" \
+        -e "s|@BANDICOOT_LIBS@|${BANDICOOT_LIBS}|g" \
+        -e "s|@OPENMP_CXXFLAGS@|${OPENMP_CXXFLAGS}|g" \
+        -e "s|@OPENCL_TARGET_VERSION@|${OPENCL_TARGET_VERSION}|g" \
+        -e "s|@BANDICOOT_KERNELS_DIR@|${BANDICOOT_KERNELS_DIR}|g" \
+        src/Makevars.win.in > src/Makevars.win
+    echo "Generated src/Makevars.win"
+else
+    echo "ERROR: src/Makevars.win.in not found!"
+    exit 1
+fi
+
+## Verify the generated file
+if [ -f "src/Makevars.win" ]; then
+    echo "Contents of src/Makevars.win:"
+    cat src/Makevars.win
+else
+    echo "ERROR: Failed to generate src/Makevars.win!"
+    exit 1
+fi
+
+## Generate R/flags.R from template
+## Set variables for flags.R.in substitution
+HAVE_CUDA=0
+HAVE_OPENMP=1
+DEFAULT_BACKEND="CL_BACKEND"
+OPENCL_CXXFLAGS_FOR_R=""
+OPENCL_LIBS_FOR_R=""
+CUDA_CXXFLAGS=""
+CUDA_LIBS=""
+CLBLAST_CXXFLAGS_FOR_R=""
+CLBLAST_LIBS_FOR_R=""
+CLBLAS_CXXFLAGS=""
+CLBLAS_LIBS=""
+LAPACK_BLAS_LIBS="\$(LAPACK_LIBS) \$(BLAS_LIBS) \$(FLIBS)"
+CLBLAST_PREFIX=""
+CLBLAS_PREFIX=""
+CUDA_HOME=""
+SDKPATH=""
+
+## Set OpenCL flags for R if detected
+if [ "${HAVE_OPENCL}" = "1" ]; then
+    OPENCL_CXXFLAGS_FOR_R="-DCOOT_USE_OPENCL ${OPENCL_CPPFLAGS}"
+    OPENCL_LIBS_FOR_R="${OPENCL_LIBS}"
+fi
+
+## Set CLBlast flags for R if detected
+if [ "${HAVE_CLBLAST}" = "1" ]; then
+    CLBLAST_CXXFLAGS_FOR_R="-DCOOT_USE_CLBLAST ${CLBLAST_CPPFLAGS}"
+    CLBLAST_LIBS_FOR_R="${CLBLAST_LIBS}"
+fi
+
+if [ -f "R/flags.R.in" ]; then
+    sed -e "s|@BANDICOOT_CXXFLAGS@|${BANDICOOT_CXXFLAGS}|g" \
+        -e "s|@BANDICOOT_LIBS@|${BANDICOOT_LIBS}|g" \
+        -e "s|@OPENCL_CXXFLAGS@|${OPENCL_CXXFLAGS_FOR_R}|g" \
+        -e "s|@OPENCL_LIBS@|${OPENCL_LIBS_FOR_R}|g" \
+        -e "s|@CUDA_CXXFLAGS@|${CUDA_CXXFLAGS}|g" \
+        -e "s|@CUDA_LIBS@|${CUDA_LIBS}|g" \
+        -e "s|@CLBLAST_CXXFLAGS@|${CLBLAST_CXXFLAGS_FOR_R}|g" \
+        -e "s|@CLBLAST_LIBS@|${CLBLAST_LIBS_FOR_R}|g" \
+        -e "s|@CLBLAS_CXXFLAGS@|${CLBLAS_CXXFLAGS}|g" \
+        -e "s|@CLBLAS_LIBS@|${CLBLAS_LIBS}|g" \
+        -e "s|@LAPACK_BLAS_LIBS@|${LAPACK_BLAS_LIBS}|g" \
+        -e "s|@HAVE_OPENCL@|${HAVE_OPENCL}|g" \
+        -e "s|@HAVE_CUDA@|${HAVE_CUDA}|g" \
+        -e "s|@HAVE_CLBLAST@|${HAVE_CLBLAST}|g" \
+        -e "s|@HAVE_CLBLAS@|${HAVE_CLBLAS}|g" \
+        -e "s|@HAVE_OPENMP@|${HAVE_OPENMP}|g" \
+        -e "s|@DEFAULT_BACKEND@|${DEFAULT_BACKEND}|g" \
+        -e "s|@CLBLAST_PREFIX@|${CLBLAST_PREFIX}|g" \
+        -e "s|@CLBLAS_PREFIX@|${CLBLAS_PREFIX}|g" \
+        -e "s|@CUDA_HOME@|${CUDA_HOME}|g" \
+        -e "s|@SDKPATH@|${SDKPATH}|g" \
+        R/flags.R.in > R/flags.R
+    echo "Generated R/flags.R"
+else
+    echo "ERROR: R/flags.R.in not found!"
+    exit 1
+fi
diff --git a/src/.gitignore b/src/.gitignore
index 22034c4..5948b32 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1,3 +1,5 @@
 *.o
 *.so
 *.dll
+Makevars
+Makevars.win
diff --git a/src/Makevars.win b/src/Makevars.win
deleted file mode 100644
index 667e3f0..0000000
--- a/src/Makevars.win
+++ /dev/null
@@ -1,11 +0,0 @@
-## RcppBandicoot Makevars.win
-##
-## Windows-specific Makevars
-## GPU backend configuration must be done manually on Windows
-
-PKG_CPPFLAGS = -I../inst/include
-
-## Warning: GPU backends may not be properly configured
-## Users may need to manually specify OpenCL or CUDA paths
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -Wno-missing-braces
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.win.in b/src/Makevars.win.in
new file mode 100644
index 0000000..ccdda30
--- /dev/null
+++ b/src/Makevars.win.in
@@ -0,0 +1,12 @@
+## RcppBandicoot Makevars.win.in
+##
+## This file is processed by configure.win to generate Makevars.win
+## It includes GPU backend configuration (OpenCL, CLBlast) for Windows
+
+PKG_CPPFLAGS = -I../inst/include -DCOOT_TARGET_OPENCL_VERSION=@OPENCL_TARGET_VERSION@ -DCOOT_KERNEL_SOURCE_DIR=\"@BANDICOOT_KERNELS_DIR@\"
+
+## Compiler flags from configure.win
+PKG_CXXFLAGS = @BANDICOOT_CXXFLAGS@
+
+## Linker flags from configure.win
+PKG_LIBS = @OPENMP_CXXFLAGS@ @BANDICOOT_LIBS@