diff --git a/autoload/gitgutter/hunk.vim b/autoload/gitgutter/hunk.vim
index 8f939f4..a590f57 100644
--- a/autoload/gitgutter/hunk.vim
+++ b/autoload/gitgutter/hunk.vim
@@ -294,11 +294,28 @@ endfunction
 
 function! s:stage(hunk_diff)
   let bufnr = bufnr('')
-  let diff = s:adjust_header(bufnr, a:hunk_diff)
-  " Apply patch to index.
-  call gitgutter#utility#system(
-        \ gitgutter#utility#cd_cmd(bufnr, g:gitgutter_git_executable.' '.g:gitgutter_git_args.' apply --cached --unidiff-zero - '),
-        \ diff)
+
+  if s:clean_smudge_filter_applies(bufnr)
+    let choice = input('File uses clean/smudge filter. Stage entire file (y/n)? ')
+    normal! :<ESC>
+    if choice =~ 'y'
+      let path = gitgutter#utility#repo_path(bufnr, 1)
+      " Add file to index.
+      call gitgutter#utility#system(
+            \ gitgutter#utility#cd_cmd(bufnr, g:gitgutter_git_executable.' '.g:gitgutter_git_args.' add '.path)
+            \ )
+    else
+      return
+    endif
+
+  else
+    let diff = s:adjust_header(bufnr, a:hunk_diff)
+    " Apply patch to index.
+    call gitgutter#utility#system(
+          \ gitgutter#utility#cd_cmd(bufnr, g:gitgutter_git_executable.' '.g:gitgutter_git_args.' apply --cached --unidiff-zero - '),
+          \ diff)
+  endif
+
   if v:shell_error
     call gitgutter#utility#warn('Patch does not apply')
   else
@@ -637,3 +654,17 @@ function gitgutter#hunk#is_preview_window_open()
   endif
   return 0
 endfunction
+
+
+function! s:clean_smudge_filter_applies(bufnr)
+  let filtered = gitgutter#utility#getbufvar(a:bufnr, 'filter', -1)
+  if filtered == -1
+    let path = gitgutter#utility#repo_path(a:bufnr, 1)
+    let out = gitgutter#utility#system(
+          \ gitgutter#utility#cd_cmd(a:bufnr, g:gitgutter_git_executable.' '.g:gitgutter_git_args.' check-attr filter -- '.path)
+          \ )
+    let filtered = out !~ 'unspecified'
+    call gitgutter#utility#setbufvar(a:bufnr, 'filter', filtered)
+  endif
+  return filtered
+endfunction