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"
@@ -221,8 +222,9 @@
   }
 
   // Assign addresses as instructed by linker script SECTIONS sub-commands.
-  Dot = Out<ELFT>::ElfHeader->getSize() + Out<ELFT>::ProgramHeaders->getSize();
-  uintX_t ThreadBssOffset = 0;
+  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) {
     if (Cmd.Kind == ExprKind) {
@@ -248,11 +250,17 @@
       if (Sec->getFlags() & SHF_ALLOC) {
         Dot = alignTo(Dot, Sec->getAlignment());
         Sec->setVA(Dot);
+        MinVA = std::min(MinVA, Dot);
         Dot += Sec->getSize();
         continue;
       }
     }
   }
+
+  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
@@ -1186,6 +1186,14 @@
   uintX_t Off =
       Out<ELFT>::ElfHeader->getSize() + Out<ELFT>::ProgramHeaders->getSize();
 
+  if (ScriptConfig->DoLayout && OutputSections.size()) {
+    // File offsets should always be equal section virtual addresses 
+    // modulo page size. In case linker script is used we enforce this constraint
+    // for ELF headers here
+    OutputSectionBase<ELFT> *Sec = OutputSections.front();
+    Off = Sec->getVA() - alignDown(Sec->getVA() - Off, Target->PageSize);
+  }
+  
   for (OutputSectionBase<ELFT> *Sec : OutputSections) {
     if (Sec->getType() == SHT_NOBITS) {
       Sec->setFileOffset(Off);
@@ -1227,7 +1235,7 @@
       Out<ELFT>::TlsPhdr = &H;
       H.p_memsz = alignTo(H.p_memsz, H.p_align);
     }
-  }
+  }  
 }
 
 static uint32_t getMipsEFlags(bool Is64Bits) {
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
+