Index: ELF/LinkerScript.cpp
===================================================================
--- ELF/LinkerScript.cpp
+++ ELF/LinkerScript.cpp
@@ -20,6 +20,7 @@
 #include "OutputSections.h"
 #include "ScriptParser.h"
 #include "SymbolTable.h"
+#include "Target.h"
 #include "llvm/ADT/StringSwitch.h"
 #include "llvm/Support/ELF.h"
 #include "llvm/Support/FileSystem.h"
@@ -222,6 +223,7 @@
 
   // Assign addresses as instructed by linker script SECTIONS sub-commands.
   Dot = Out<ELFT>::ElfHeader->getSize() + Out<ELFT>::ProgramHeaders->getSize();
+  uintX_t MinVA = std::numeric_limits<uintX_t>::max();
   uintX_t ThreadBssOffset = 0;
 
   for (SectionsCommand &Cmd : Opt.Commands) {
@@ -248,11 +250,19 @@
       if (Sec->getFlags() & SHF_ALLOC) {
         Dot = alignTo(Dot, Sec->getAlignment());
         Sec->setVA(Dot);
+        MinVA = std::min(MinVA, Dot);
         Dot += Sec->getSize();
         continue;
       }
     }
   }
+  
+  // ELF and Program headers need to be right before the first section in memory.
+  // Set their addresses accordingly.
+  MinVA = alignDown(MinVA - Out<ELFT>::ElfHeader->getSize() - 
+                    Out<ELFT>::ProgramHeaders->getSize(), Target->PageSize);
+  Out<ELFT>::ElfHeader->setVA(MinVA);
+  Out<ELFT>::ProgramHeaders->setVA(Out<ELFT>::ElfHeader->getSize() + MinVA);  
 }
 
 template <class ELFT>
Index: ELF/Writer.cpp
===================================================================
--- ELF/Writer.cpp
+++ ELF/Writer.cpp
@@ -1132,10 +1132,8 @@
 template <class ELFT> void Writer<ELFT>::fixHeaders() {
   uintX_t BaseVA = ScriptConfig->DoLayout ? 0 : Target->getVAStart();
   Out<ELFT>::ElfHeader->setVA(BaseVA);
-  Out<ELFT>::ElfHeader->setFileOffset(0);
   uintX_t Off = Out<ELFT>::ElfHeader->getSize();
   Out<ELFT>::ProgramHeaders->setVA(Off + BaseVA);
-  Out<ELFT>::ProgramHeaders->setFileOffset(Off);
 }
 
 // Assign VAs (addresses at run-time) to output sections.
@@ -1183,19 +1181,25 @@
 
 // Assign file offsets to output sections.
 template <class ELFT> void Writer<ELFT>::assignFileOffsets() {
-  uintX_t Off =
-      Out<ELFT>::ElfHeader->getSize() + Out<ELFT>::ProgramHeaders->getSize();
+  uintX_t Off = 0;
 
-  for (OutputSectionBase<ELFT> *Sec : OutputSections) {
+  auto Set = [&](OutputSectionBase<ELFT> *Sec) {
     if (Sec->getType() == SHT_NOBITS) {
+      if (Sec == OutputSections.front())
+        Off = getFileAlignment<ELFT>(Off, Sec);
       Sec->setFileOffset(Off);
-      continue;
+      return;
     }
-
     Off = getFileAlignment<ELFT>(Off, Sec);
     Sec->setFileOffset(Off);
     Off += Sec->getSize();
-  }
+  };
+  
+  Set(Out<ELFT>::ElfHeader);
+  Set(Out<ELFT>::ProgramHeaders);
+  for (OutputSectionBase<ELFT> *Sec : OutputSections)
+    Set(Sec);
+  
   SectionHeaderOff = alignTo(Off, sizeof(uintX_t));
   FileSize = SectionHeaderOff + (OutputSections.size() + 1) * sizeof(Elf_Shdr);
 }
Index: test/ELF/linkerscript-phdr-check.s
===================================================================
--- test/ELF/linkerscript-phdr-check.s
+++ test/ELF/linkerscript-phdr-check.s
@@ -0,0 +1,16 @@
+# REQUIRES: x86
+# RUN: llvm-mc -filetype=obj -triple=x86_64-unknown-linux %s -o %t
+
+# RUN: echo "SECTIONS { . = 0x10000000; .text : {*(.text.*)} }" > %t.script
+# RUN: ld.lld -o %t1 --script %t.script %t
+# RUN: llvm-readobj -program-headers %t1 | FileCheck %s
+# CHECK:      ProgramHeaders [
+# CHECK-NEXT:  ProgramHeader {
+# CHECK-NEXT:    Type: PT_PHDR (0x6)
+# CHECK-NEXT:    Offset: 0x40
+# CHECK-NEXT:    VirtualAddress: 0xFFFF040
+
+.global _start
+_start:
+ nop
+