diff --git a/tools/build_api.py b/tools/build_api.py
index c769dea202..9531967992 100644
--- a/tools/build_api.py
+++ b/tools/build_api.py
@@ -20,6 +20,9 @@ import re
 import tempfile
 import datetime
 import uuid
+import struct
+import zlib
+import hashlib
 from shutil import rmtree
 from os.path import join, exists, dirname, basename, abspath, normpath, splitext
 from os.path import relpath
@@ -339,8 +342,65 @@ def prepare_toolchain(src_paths, build_dir, target, toolchain_name,
 
     return toolchain
 
+def _printihex(ihex):
+    import pprint
+    pprint.PrettyPrinter().pprint(ihex.todict())
+
+def _real_region_size(region):
+    try:
+        part = intelhex_offset(region.filename, offset=region.start)
+        return (part.maxaddr() - part.minaddr()) + 1
+    except AttributeError:
+        return region.size
+
+def _fill_header(region_list, current_region):
+    """Fill an application header region
+
+    This is done it three steps:
+     * Fill the whole region with zeros
+     * Fill const, timestamp and size entries with their data
+     * Fill the digests using this header as the header region
+    """
+    region_dict = {r.name: r for r in region_list}
+    header = IntelHex()
+    header.puts(current_region.start, b'\x00' * current_region.size)
+    start = current_region.start
+    for member in current_region.filename:
+        _, type, subtype, data = member
+        member_size = Config.header_member_size(member)
+        if type == "const":
+            fmt = {"8": "<B", "16": "<H", "32": "<L", "64": "<Q"}[subtype]
+            header.puts(start, struct.pack(fmt, int(data, 0)))
+        elif type == "timestamp":
+            fmt = {"32": "<L", "64": "<Q"}[subtype]
+            header.puts(start, struct.pack(fmt, time()))
+        elif type == "size":
+            fmt = {"32": "<L", "64": "<Q"}[subtype]
+            size = sum(_real_region_size(region_dict[r]) for r in data)
+            header.puts(start, struct.pack(fmt, size))
+        start += Config.header_member_size(member)
+    start = current_region.start
+    for member in current_region.filename:
+        _, type, subtype, data = member
+        if type  == "digest":
+            if data == "header":
+                ih = header
+            else:
+                ih = intelhex_offset(region_dict[data].filename, offset=region_dict[data].start)
+            if subtype == "CRCITT32":
+                header.puts(start, struct.pack("<l", zlib.crc32(ih.tobinarray())))
+            elif subtype.startswith("SHA"):
+                if subtype == "SHA256":
+                    hash = hashlib.sha256()
+                elif subtype == "SHA512":
+                    hash = hashlib.sha512()
+                hash.update(ih.tobinarray())
+                header.puts(start, hash.digest())
+        start += Config.header_member_size(member)
+    return header
+
 def merge_region_list(region_list, destination, padding=b'\xFF'):
-    """Merege the region_list into a single image
+    """Merge the region_list into a single image
 
     Positional Arguments:
     region_list - list of regions, which should contain filenames
@@ -355,6 +415,11 @@ def merge_region_list(region_list, destination, padding=b'\xFF'):
     for region in region_list:
         if region.active and not region.filename:
             raise ToolException("Active region has no contents: No file found.")
+        if isinstance(region.filename, list):
+            header_basename, _ = splitext(destination)
+            header_filename = header_basename + "_header.hex"
+            _fill_header(region_list, region).tofile(header_filename, format='hex')
+            region = region._replace(filename=header_filename)
         if region.filename:
             print("  Filling region %s with %s" % (region.name, region.filename))
             part = intelhex_offset(region.filename, offset=region.start)
diff --git a/tools/config/__init__.py b/tools/config/__init__.py
index 07a57343ac..673d9e490f 100644
--- a/tools/config/__init__.py
+++ b/tools/config/__init__.py
@@ -569,25 +569,29 @@ class Config(object):
             raise ConfigException(
                 "Bootloader build requested but no bootlader configuration")
 
+    @staticmethod
+    def header_member_size(member):
+        _, _, subtype, _ = member
+        try:
+            return int(subtype) // 8
+        except:
+            if subtype == "CRCITT32":
+                return 32 // 8
+            elif subtype == "SHA256":
+                return 256 // 8
+            elif subtype == "SHA512":
+                return 512 // 8
+            else:
+                raise ValueError("target.header_format: subtype %s is not "
+                                 "understood" % subtype)
+
     @staticmethod
     def _header_size(format):
-        size_in_bytes = 0
-        for _, _, subtype, _ in format:
-            try:
-                size_in_bytes += int(subtype) // 8
-            except:
-                if subtype == "CRCITT32":
-                    size_in_bytes += 32 // 8
-                elif subtype == "SHA256":
-                    size_in_bytes += 256 // 8
-                else:
-                    raise ValueError("target.header_format: subtype %s is not "
-                                     "understood" % subtype)
-        return size_in_bytes
+        return sum(Config.header_member_size(m) for m in format)
 
     def _make_header_region(self, start, header_format):
         size = self._header_size(header_format)
-        region = Region("application_header", start, size, False, None)
+        region = Region("header", start, size, False, None)
         start += size
         start = ((start + 7) // 8) * 8
         return (start, region)
@@ -615,7 +619,7 @@ class Config(object):
             if self.target.header_format:
                 start, region = self._make_header_region(
                     start, self.target.header_format)
-                yield region
+                yield region._replace(filename=self.target.header_format)
         if self.target.restrict_size is not None:
             new_size = int(self.target.restrict_size, 0)
             new_size = Config._align_floor(start + new_size, self.sectors) - start