Index: lld/trunk/ELF/Writer.cpp
===================================================================
--- lld/trunk/ELF/Writer.cpp
+++ lld/trunk/ELF/Writer.cpp
@@ -1662,6 +1662,24 @@
   }
 }
 
+// Adjusts the file alignment for a given output section and returns
+// its new file offset. The file offset must be the same with its
+// virtual address (modulo the page size) so that the loader can load
+// executables without any address adjustment.
+template <class ELFT, class uintX_t>
+static uintX_t getFileAlignment(uintX_t Off, OutputSectionBase<ELFT> *Sec) {
+  uintX_t Align = Sec->getAlign();
+  if (Sec->PageAlign)
+    Align = std::max<uintX_t>(Align, Target->PageSize);
+  Off = alignTo(Off, Align);
+
+  // Relocatable output does not have program headers
+  // and does not need any other offset adjusting.
+  if (Config->Relocatable || !(Sec->getFlags() & SHF_ALLOC))
+    return Off;
+  return alignTo(Off, Target->PageSize, Sec->getVA());
+}
+
 // Assign file offsets to output sections.
 template <class ELFT> void Writer<ELFT>::assignFileOffsets() {
   uintX_t Off =
@@ -1672,10 +1690,8 @@
       Sec->setFileOffset(Off);
       continue;
     }
-    uintX_t Align = Sec->getAlign();
-    if (Sec->PageAlign)
-      Align = std::max<uintX_t>(Align, Target->PageSize);
-    Off = alignTo(Off, Align);
+
+    Off = getFileAlignment<ELFT>(Off, Sec);
     Sec->setFileOffset(Off);
     Off += Sec->getSize();
   }
Index: lld/trunk/test/ELF/phdr-align.s
===================================================================
--- lld/trunk/test/ELF/phdr-align.s
+++ lld/trunk/test/ELF/phdr-align.s
@@ -0,0 +1,82 @@
+# REQUIRES: x86
+# RUN: llvm-mc -filetype=obj -triple=x86_64-pc-linux %s -o %t.o
+
+# RUN: echo "SECTIONS { \
+# RUN:  .bss : { *(.bss) } \
+# RUN:  .data : { *(.data) } \
+# RUN:  .text : { *(.text) } }" > %t.script
+# RUN: ld.lld %t.o --script %t.script -o %t
+# RUN: llvm-readobj -sections -symbols %t | FileCheck %s
+
+# CHECK:      Sections [
+# CHECK-NEXT:  Section {
+# CHECK-NEXT:    Index: 0
+# CHECK-NEXT:    Name:  (0)
+# CHECK-NEXT:    Type: SHT_NULL
+# CHECK-NEXT:    Flags [
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Address: 0x0
+# CHECK-NEXT:    Offset: 0x0
+# CHECK-NEXT:    Size: 0
+# CHECK-NEXT:    Link: 0
+# CHECK-NEXT:    Info: 0
+# CHECK-NEXT:    AddressAlignment: 0
+# CHECK-NEXT:    EntrySize: 0
+# CHECK-NEXT:  }
+# CHECK-NEXT:  Section {
+# CHECK-NEXT:    Index: 1
+# CHECK-NEXT:    Name: .bss
+# CHECK-NEXT:    Type: SHT_NOBITS
+# CHECK-NEXT:    Flags [
+# CHECK-NEXT:      SHF_ALLOC
+# CHECK-NEXT:      SHF_WRITE
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Address: 0x158
+# CHECK-NEXT:    Offset: 0x158
+# CHECK-NEXT:    Size: 6
+# CHECK-NEXT:    Link: 0
+# CHECK-NEXT:    Info: 0
+# CHECK-NEXT:    AddressAlignment: 1
+# CHECK-NEXT:    EntrySize: 0
+# CHECK-NEXT:  }
+# CHECK-NEXT:  Section {
+# CHECK-NEXT:    Index: 2
+# CHECK-NEXT:    Name: .data
+# CHECK-NEXT:    Type: SHT_PROGBITS
+# CHECK-NEXT:    Flags [
+# CHECK-NEXT:      SHF_ALLOC
+# CHECK-NEXT:      SHF_WRITE
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Address: 0x15E
+# CHECK-NEXT:    Offset: 0x15E
+# CHECK-NEXT:    Size: 2
+# CHECK-NEXT:    Link: 0
+# CHECK-NEXT:    Info: 0
+# CHECK-NEXT:    AddressAlignment: 1
+# CHECK-NEXT:    EntrySize: 0
+# CHECK-NEXT:  }
+# CHECK-NEXT:  Section {
+# CHECK-NEXT:    Index: 3
+# CHECK-NEXT:    Name: .text
+# CHECK-NEXT:    Type: SHT_PROGBITS
+# CHECK-NEXT:    Flags [
+# CHECK-NEXT:      SHF_ALLOC
+# CHECK-NEXT:      SHF_EXECINSTR
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Address: 0x160
+# CHECK-NEXT:    Offset: 0x160
+# CHECK-NEXT:    Size: 1
+# CHECK-NEXT:    Link: 0
+# CHECK-NEXT:    Info: 0
+# CHECK-NEXT:    AddressAlignment: 4
+# CHECK-NEXT:    EntrySize: 0
+# CHECK-NEXT:  }
+
+.global _start
+.text
+_start:
+ nop
+.data
+ .word 1
+.bss
+ .space 6