diff --git a/lib/bats-core/test_functions.bash b/lib/bats-core/test_functions.bash
index e9fdeb05..1301ff34 100644
--- a/lib/bats-core/test_functions.bash
+++ b/lib/bats-core/test_functions.bash
@@ -29,18 +29,121 @@ load() {
   source "${file}"
 }
 
-run() {
+bats_suppress_stderr() {
+  "$@" 2>/dev/null
+}
+
+bats_suppress_stdout() {
+  # throw away stdout and redirect stderr into stdout
+  # shellcheck disable=SC2069
+  "$@" 2>&1 >/dev/null 
+}
+
+bats_redirect_stderr_into_file() {
+  "$@" 2>>"$bats_run_separate_stderr_file" # use >> to see collisions' content
+}
+
+bats_merge_stdout_and_stderr() {
+  "$@" 2>&1
+}
+
+# write separate lines from <input-var> into <output-array>
+bats_separate_lines() { # <output-array> <input-var>
+  output_array_name="$1"
+  input_var_name="$2"
+  if [[ $keep_empty_lines ]]; then
+    local bats_separate_lines_lines=()
+    while IFS= read -r line; do
+      bats_separate_lines_lines+=("$line")
+    done <<<"${!input_var_name}"
+    eval "${output_array_name}=(\"\${bats_separate_lines_lines[@]}\")"
+  else
+    # shellcheck disable=SC2034,SC2206
+    IFS=$'\n' read -d '' -r -a "$output_array_name" <<<"${!input_var_name}"
+  fi
+}
+
+run() { # [--keep-empty-lines] [--output merged|separate|stderr|stdout] [--] <command to run...>
   trap bats_interrupt_trap_in_run INT
+  local keep_empty_lines=
+  local output_case=merged
+  # parse options starting with -
+  while [[ $# -gt 0 && $1 == -* ]]; do
+    case "$1" in
+      --keep-empty-lines)
+        keep_empty_lines=1
+      ;;
+      --output)
+        output_case="$2"
+        shift 2 # consume the value too!
+      ;;
+      --)
+        shift # eat the -- before breaking away
+        break
+      ;;
+    esac
+    shift
+  done
+
+  local pre_command=
+
+  case "$output_case" in
+    merged) # redirects stderr into stdout and fills only $output/$lines
+      pre_command=bats_merge_stdout_and_stderr
+    ;;
+    separate) # splits stderr into own file and fills $stderr/$stderr_lines too
+      local bats_run_separate_stderr_file
+      bats_run_separate_stderr_file="$(mktemp "${BATS_TEST_TMPDIR}/separate-stderr-XXXXXX")"
+      pre_command=bats_redirect_stderr_into_file
+    ;;
+    stderr) # suppresses stdout and fills $stderr/$stderr_lines
+      pre_command=bats_suppress_stdout
+    ;;
+    stdout) # suppresses stderr and fills $output/$lines
+      pre_command=bats_suppress_stderr
+    ;;
+    *)
+      printf "ERROR: Unknown --output value %s" "$output_case"
+      return 1
+    ;;
+  esac
+
   local origFlags="$-"
   set -f +eET
   local origIFS="$IFS"
-  # 'output', 'status', 'lines' are global variables available to tests.
-  # shellcheck disable=SC2034
-  output="$("$@" 2>&1)"
-  # shellcheck disable=SC2034
-  status="$?"
-  # shellcheck disable=SC2034,SC2206
-  IFS=$'\n' lines=($output)
+  if [[ $keep_empty_lines ]]; then
+    # 'output', 'status', 'lines' are global variables available to tests.
+    # preserve trailing newlines by appending . and removing it later
+    # shellcheck disable=SC2034
+    output="$($pre_command "$@"; status=$?; printf .; exit $status)"
+    # shellcheck disable=SC2034
+    status="$?"
+    output="${output%.}"
+  else
+    # 'output', 'status', 'lines' are global variables available to tests.
+    # shellcheck disable=SC2034
+    output="$($pre_command "$@")"
+    # shellcheck disable=SC2034
+    status="$?"
+  fi
+
+  bats_separate_lines lines output
+
+  case "$output_case" in
+    stderr)
+      stderr="$output"
+      # shellcheck disable=SC2034
+      stderr_lines=("${lines[@]}")
+      unset output
+      unset lines
+    ;;
+    separate)
+      # shellcheck disable=SC2034
+      read -d '' -r stderr < "$bats_run_separate_stderr_file"
+      bats_separate_lines stderr_lines stderr
+    ;;
+  esac
+
   IFS="$origIFS"
   set "-$origFlags"
 }
diff --git a/test/run.bats b/test/run.bats
new file mode 100644
index 00000000..b87d88a1
--- /dev/null
+++ b/test/run.bats
@@ -0,0 +1,76 @@
+@test "run --keep-empty-lines preserves leading empty lines" {
+    run --keep-empty-lines -- echo -n $'\na'
+    printf "'%s'\n" "${lines[@]}"
+    [ "${lines[0]}" == '' ]
+    [ "${lines[1]}" == a ]
+    [ ${#lines[@]} -eq 2 ]
+}
+
+@test "run --keep-empty-lines preserves inner empty lines" {
+    run --keep-empty-lines -- echo -n $'a\n\nb'
+    printf "'%s'\n" "${lines[@]}"
+    [ "${lines[0]}" == a ]
+    [ "${lines[1]}" == '' ]
+    [ "${lines[2]}" == b ]
+    [ ${#lines[@]} -eq 3 ]
+}
+
+@test "run --keep-empty-lines preserves trailing empty lines" {
+    run --keep-empty-lines -- echo -n $'a\n'
+    printf "'%s'\n" "${lines[@]}"
+    [ "${lines[0]}" == a ]
+    [ "${lines[1]}" == '' ]
+    [ ${#lines[@]} -eq 2 ]
+}
+
+@test "run --keep-empty-lines preserves multiple trailing empty lines" {
+    run --keep-empty-lines -- echo -n $'a\n\n'
+    printf "'%s'\n" "${lines[@]}"
+    [ "${lines[0]}" == a ]
+    [ "${lines[1]}" == '' ]
+    [ "${lines[2]}" == '' ]
+    [ ${#lines[@]} -eq 3 ]
+}
+
+@test "run --keep-empty-lines preserves non-empty trailing line" {
+    run --keep-empty-lines -- echo -n $'a\nb'
+    printf "'%s'\n" "${lines[@]}"
+    [ "${lines[0]}" == a ]
+    [ "${lines[1]}" == b ]
+    [ ${#lines[@]} -eq 2 ]
+}
+
+print-stderr-stdout() {
+    printf stdout
+    printf stderr >&2
+}
+
+@test "run --output stdout does not print stderr" {   
+    run --output stdout -- print-stderr-stdout
+    echo "output='$output' stderr='$stderr'"
+    [ "$output" = "stdout" ]
+    [ ${#lines[@]} -eq 1 ]
+
+    [ "${stderr-notset}" = notset ]
+    [ ${#stderr_lines[@]} -eq 0 ]
+}
+
+@test "run --output stderr does not print stdout" {
+    run --output stderr -- print-stderr-stdout
+    echo "output='$output' stderr='$stderr'"
+    [ "${output-notset}" = notset ]
+    [ ${#lines[@]} -eq 0 ]
+
+    [ "$stderr" = stderr ]
+    [ ${#stderr_lines[@]} -eq 1 ]
+}
+
+@test "run --output separate splits output" {
+    run --output separate -- print-stderr-stdout
+    echo "output='$output' stderr='$stderr'"
+    [ "$output" = stdout ]
+    [ ${#lines[@]} -eq 1 ]
+
+    [ "$stderr" = stderr ]
+    [ ${#stderr_lines[@]} -eq 1 ]
+}
\ No newline at end of file