Index: cmake/Modules/CheckLibcxxAtomic.cmake
===================================================================
--- cmake/Modules/CheckLibcxxAtomic.cmake
+++ cmake/Modules/CheckLibcxxAtomic.cmake
@@ -9,10 +9,13 @@
 
 function(check_cxx_atomics varname)
   set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
-  set(CMAKE_REQUIRED_FLAGS "-std=c++11 -nostdinc++ -isystem ${LIBCXX_SOURCE_DIR}/include")
+  set(CMAKE_REQUIRED_FLAGS "-nodefaultlibs -std=c++11 -nostdinc++ -isystem ${LIBCXX_SOURCE_DIR}/include")
   if (${LIBCXX_GCC_TOOLCHAIN})
     set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} --gcc-toolchain=${LIBCXX_GCC_TOOLCHAIN}")
   endif()
+  if (CMAKE_C_FLAGS MATCHES -fsanitize OR CMAKE_CXX_FLAGS MATCHES -fsanitize)
+    set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} -fno-sanitize=all")
+  endif()
   check_cxx_source_compiles("
 #include <cstdint>
 #include <atomic>
Index: cmake/config-ix.cmake
===================================================================
--- cmake/config-ix.cmake
+++ cmake/config-ix.cmake
@@ -1,5 +1,34 @@
 include(CheckLibraryExists)
 include(CheckCXXCompilerFlag)
+
+check_library_exists(c fopen "" LIBCXX_HAS_C_LIB)
+if (NOT LIBCXX_USE_COMPILER_RT)
+  check_library_exists(gcc_s __gcc_personality_v0 "" LIBCXX_HAS_GCC_S_LIB)
+endif()
+
+# libc++ is built with -nodefaultlibs, so we want all our checks to also
+# use this option, otherwise we may end up with an inconsistency between
+# the flags we think we require during configuration (if the checks are
+# performed without -nodefaultlibs) and the flags that are actually
+# required during compilation (which has the -nodefaultlibs). libc is
+# required for the link to go through. We remove sanitizers from the
+# configuration checks to avoid spurious link errors.
+check_cxx_compiler_flag(-nodefaultlibs LIBCXX_SUPPORTS_NODEFAULTLIBS_FLAG)
+if (LIBCXX_SUPPORTS_NODEFAULTLIBS_FLAG)
+  set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} -nodefaultlibs")
+  if (LIBCXX_HAS_C_LIB)
+    list(APPEND CMAKE_REQUIRED_LIBRARIES c)
+  endif ()
+  if (LIBCXX_USE_COMPILER_RT)
+    list(APPEND CMAKE_REQUIRED_LIBRARIES -rtlib=compiler-rt)
+  elseif (LIBCXX_HAS_GCC_S_LIB)
+    list(APPEND CMAKE_REQUIRED_LIBRARIES gcc_s)
+  endif ()
+  if (CMAKE_C_FLAGS MATCHES -fsanitize OR CMAKE_CXX_FLAGS MATCHES -fsanitize)
+    set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} -fno-sanitize=all")
+  endif ()
+endif ()
+
 include(CheckLibcxxAtomic)
 
 # Check compiler flags
@@ -14,9 +43,5 @@
 
 # Check libraries
 check_library_exists(pthread pthread_create "" LIBCXX_HAS_PTHREAD_LIB)
-check_library_exists(c fopen "" LIBCXX_HAS_C_LIB)
 check_library_exists(m ccos "" LIBCXX_HAS_M_LIB)
 check_library_exists(rt clock_gettime "" LIBCXX_HAS_RT_LIB)
-if (NOT LIBCXX_USE_COMPILER_RT)
-  check_library_exists(gcc_s __gcc_personality_v0 "" LIBCXX_HAS_GCC_S_LIB)
-endif()