diff --git a/csharp/generate_protos.sh b/csharp/generate_protos.sh
index 0d217a9de6..3a556b0e3f 100755
--- a/csharp/generate_protos.sh
+++ b/csharp/generate_protos.sh
@@ -35,11 +35,10 @@ if [ -z "$PROTOC" ]; then
   fi
 fi
 
-# Descriptor proto
-$PROTOC -Isrc --csharp_out=csharp/src/Google.Protobuf/Reflection \
-    src/google/protobuf/descriptor.proto
-
-$PROTOC -Isrc --csharp_out=csharp/src/Google.Protobuf/WellKnownTypes \
+# descriptor.proto and well-known types
+$PROTOC -Isrc --csharp_out=csharp/src/Google.Protobuf \
+    --csharp_opt=base_namespace=Google.Protobuf \
+    src/google/protobuf/descriptor.proto \
     src/google/protobuf/any.proto \
     src/google/protobuf/api.proto \
     src/google/protobuf/duration.proto \
@@ -51,15 +50,18 @@ $PROTOC -Isrc --csharp_out=csharp/src/Google.Protobuf/WellKnownTypes \
     src/google/protobuf/type.proto \
     src/google/protobuf/wrappers.proto
 
-$PROTOC -Isrc --csharp_out=csharp/src/Google.Protobuf.Test/TestProtos \
+# Test protos where the namespace matches the target location
+$PROTOC -Isrc --csharp_out=csharp/src/Google.Protobuf.Test \
+    --csharp_opt=base_namespace=Google.Protobuf \
     src/google/protobuf/map_unittest_proto3.proto \
     src/google/protobuf/unittest_proto3.proto \
     src/google/protobuf/unittest_import_proto3.proto \
     src/google/protobuf/unittest_import_public_proto3.proto \
     src/google/protobuf/unittest_well_known_types.proto
 
-
-$PROTOC -Icsharp/protos --csharp_out=csharp/src/Google.Protobuf.Test/TestProtos \
+# Different base namespace to the protos above
+$PROTOC -Icsharp/protos --csharp_out=csharp/src/Google.Protobuf.Test \
+    --csharp_opt=base_namespace=UnitTest.Issues \
     csharp/protos/unittest_issues.proto
 
 # AddressBook sample protos
diff --git a/src/google/protobuf/compiler/csharp/csharp_generator.cc b/src/google/protobuf/compiler/csharp/csharp_generator.cc
index e0a6c83a33..95ff48aeeb 100644
--- a/src/google/protobuf/compiler/csharp/csharp_generator.cc
+++ b/src/google/protobuf/compiler/csharp/csharp_generator.cc
@@ -36,10 +36,12 @@
 #include <google/protobuf/descriptor.pb.h>
 #include <google/protobuf/io/printer.h>
 #include <google/protobuf/io/zero_copy_stream.h>
+#include <google/protobuf/stubs/strutil.h>
 
 #include <google/protobuf/compiler/csharp/csharp_generator.h>
-#include <google/protobuf/compiler/csharp/csharp_umbrella_class.h>
 #include <google/protobuf/compiler/csharp/csharp_helpers.h>
+#include <google/protobuf/compiler/csharp/csharp_names.h>
+#include <google/protobuf/compiler/csharp/csharp_umbrella_class.h>
 
 using google::protobuf::internal::scoped_ptr;
 
@@ -48,9 +50,39 @@ namespace protobuf {
 namespace compiler {
 namespace csharp {
 
-std::string GetOutputFile(const google::protobuf::FileDescriptor* file, const std::string file_extension)
-{
-  return GetUmbrellaClassUnqualifiedName(file) + file_extension;
+std::string GetOutputFile(
+    const google::protobuf::FileDescriptor* file,
+    const std::string file_extension,
+    const bool generate_directories,
+    const std::string base_namespace,
+    string* error) {
+  string relative_filename = GetUmbrellaClassUnqualifiedName(file) + file_extension;
+  if (!generate_directories) {
+    return relative_filename;
+  }
+  string ns = GetFileNamespace(file);
+  string namespace_suffix = ns;
+  if (!base_namespace.empty()) {
+    // Check that the base_namespace is either equal to or a leading part of
+    // the file namespace. This isn't just a simple prefix; "Foo.B" shouldn't
+    // be regarded as a prefix of "Foo.Bar". The simplest option is to add "."
+    // to both.
+    string extended_ns = ns + ".";
+    if (extended_ns.find(base_namespace + ".") != 0) {
+      *error = "Namespace " + ns + " is not a prefix namespace of base namespace " + base_namespace;
+      return ""; // This will be ignored, because we've set an error.
+    }
+    namespace_suffix = ns.substr(base_namespace.length());
+    if (namespace_suffix.find(".") == 0) {
+      namespace_suffix = namespace_suffix.substr(1);
+    }
+  }
+
+  string namespace_dir = StringReplace(namespace_suffix, ".", "/", true);
+  if (!namespace_dir.empty()) {
+    namespace_dir += "/";
+  }
+  return namespace_dir + relative_filename;
 }
 
 void GenerateFile(const google::protobuf::FileDescriptor* file,
@@ -75,16 +107,26 @@ bool Generator::Generate(
   }
 
   std::string file_extension = ".cs";
+  std::string base_namespace = "";
+  bool generate_directories = false;
   for (int i = 0; i < options.size(); i++) {
     if (options[i].first == "file_extension") {
       file_extension = options[i].second;
+    } else if (options[i].first == "base_namespace") {
+      base_namespace = options[i].second;
+      generate_directories = true;
     } else {
       *error = "Unknown generator option: " + options[i].first;
       return false;
     }
   }
 
-  std::string filename = GetOutputFile(file, file_extension);
+  string filename_error = "";
+  std::string filename = GetOutputFile(file, file_extension, generate_directories, base_namespace, &filename_error);
+  if (!filename_error.empty()) {
+    *error = filename_error;
+    return false;
+  }
   scoped_ptr<io::ZeroCopyOutputStream> output(
       generator_context->Open(filename));
   io::Printer printer(output.get(), '$');
diff --git a/src/google/protobuf/compiler/main.cc b/src/google/protobuf/compiler/main.cc
index 4815a726fa..584e5a40df 100644
--- a/src/google/protobuf/compiler/main.cc
+++ b/src/google/protobuf/compiler/main.cc
@@ -72,7 +72,7 @@ int main(int argc, char* argv[]) {
 
   // CSharp
   google::protobuf::compiler::csharp::Generator csharp_generator;
-  cli.RegisterGenerator("--csharp_out", &csharp_generator,
+  cli.RegisterGenerator("--csharp_out", "--csharp_opt", &csharp_generator,
                         "Generate C# source file.");
 
   // Objective C