Index: ELF/Writer.cpp
===================================================================
--- ELF/Writer.cpp
+++ ELF/Writer.cpp
@@ -1638,6 +1638,29 @@
   }
 }
 
+// System V ABI 4.1 specifies that program header's
+// p_vaddr should equal p_offset, modulo p_align.
+// (http://www.x86-64.org/documentation/abi.pdf, p.76),
+// this method used to adjust sections file offsets.
+template <class ELFT, class uintX_t>
+static uintX_t alignOffset(uintX_t Off, uintX_t Align,
+                           OutputSectionBase<ELFT> *Sec) {
+  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;
+
+  uintX_t PageSize = Target->PageSize;
+  uintX_t VA = Sec->getVA();
+  if ((VA % PageSize) != (Off % PageSize)) {
+    uintX_t Val = ((Off & ~(PageSize - 1)) | (VA % PageSize));
+    Off = Val < Off ? (Val + PageSize) : Val;
+  }
+  return Off;
+}
+
 // Assign file offsets to output sections.
 template <class ELFT> void Writer<ELFT>::assignFileOffsets() {
   uintX_t Off =
@@ -1651,7 +1674,7 @@
     uintX_t Align = Sec->getAlign();
     if (Sec->PageAlign)
       Align = std::max<uintX_t>(Align, Target->PageSize);
-    Off = alignTo(Off, Align);
+    Off = alignOffset<ELFT>(Off, Align, Sec);
     Sec->setFileOffset(Off);
     Off += Sec->getSize();
   }
Index: test/ELF/phdr-align.s
===================================================================
--- test/ELF/phdr-align.s
+++ 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