diff --git a/WORKSPACE b/WORKSPACE
index 1bc607fb64f2..54c2e46b3641 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -16,11 +16,16 @@
 
 workspace(name = "drake")
 
-load("//tools/third_party/kythe/tools/build_rules/config:pkg_config.bzl", "pkg_config_package")
 load("//tools:bitbucket.bzl", "bitbucket_archive")
 load("//tools:github.bzl", "github_archive")
 load('@bazel_tools//tools/build_defs/repo:git.bzl', 'git_repository')
 
+local_repository(
+    name = "kythe",
+    path = "tools/third_party/kythe",
+)
+load("@kythe//tools/build_rules/config:pkg_config.bzl", "pkg_config_package")
+
 pkg_config_package(
     name = "glib",
     modname = "glib-2.0",
diff --git a/tools/bot_core_lcmtypes.BUILD b/tools/bot_core_lcmtypes.BUILD
index 46c3b4062208..9b91a8cc06b8 100644
--- a/tools/bot_core_lcmtypes.BUILD
+++ b/tools/bot_core_lcmtypes.BUILD
@@ -2,7 +2,7 @@
 
 package(default_visibility = ["//visibility:public"])
 
-load("@//tools:lcm.bzl", "lcm_cc_library", "lcm_py_library")
+load("@drake//tools:lcm.bzl", "lcm_cc_library", "lcm_py_library")
 
 lcm_cc_library(
     name = "bot_core_lcmtypes",
diff --git a/tools/ccd.BUILD b/tools/ccd.BUILD
index 9baafdb2caf9..114e8bfa4e41 100644
--- a/tools/ccd.BUILD
+++ b/tools/ccd.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:cmake_configure_file.bzl", "cmake_configure_file")
+load("@drake//tools:cmake_configure_file.bzl", "cmake_configure_file")
 
 # Generates config.h based on the defines= we want in Drake.
 cmake_configure_file(
diff --git a/tools/eigen.BUILD b/tools/eigen.BUILD
index 385a52e68601..9be5a170d505 100644
--- a/tools/eigen.BUILD
+++ b/tools/eigen.BUILD
@@ -1,7 +1,7 @@
 # -*- python -*-
 
-load("@//tools:install.bzl", "install", "install_files")
-load("@//tools:python_lint.bzl", "python_lint")
+load("@drake//tools:install.bzl", "install", "install_files")
+load("@drake//tools:python_lint.bzl", "python_lint")
 load("@bazel_tools//tools/build_defs/pkg:pkg.bzl", "pkg_tar")
 
 package(
@@ -25,8 +25,8 @@ cc_library(
 
 py_binary(
     name = "create-cps",
-    srcs = ["@//tools:eigen-create-cps.py"],
-    main = "@//tools:eigen-create-cps.py",
+    srcs = ["@drake//tools:eigen-create-cps.py"],
+    main = "@drake//tools:eigen-create-cps.py",
     visibility = ["//visibility:private"],
 )
 
diff --git a/tools/fcl.BUILD b/tools/fcl.BUILD
index 89185252c7f9..e39110900585 100644
--- a/tools/fcl.BUILD
+++ b/tools/fcl.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:cmake_configure_file.bzl", "cmake_configure_file")
+load("@drake//tools:cmake_configure_file.bzl", "cmake_configure_file")
 
 # Generates config.h based on the version numbers in CMake code.
 cmake_configure_file(
diff --git a/tools/gtest.BUILD b/tools/gtest.BUILD
index eebd3d145594..cdc01862d4cb 100644
--- a/tools/gtest.BUILD
+++ b/tools/gtest.BUILD
@@ -30,8 +30,8 @@ cc_library(
         "googletest/include",
     ],
     linkopts = select({
-        "@//tools:linux": ["-pthread"],
-        "@//conditions:default": [],
+        "@drake//tools:linux": ["-pthread"],
+        "@//conditions:default": [],  # This is a bazel-default rule, and does not need @drake//
     }),
     linkstatic = 1,
     visibility = ["//visibility:public"],
diff --git a/tools/ignition_math.BUILD b/tools/ignition_math.BUILD
index 5ca09bff909d..8c72d715d141 100644
--- a/tools/ignition_math.BUILD
+++ b/tools/ignition_math.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:cmake_configure_file.bzl", "cmake_configure_file")
+load("@drake//tools:cmake_configure_file.bzl", "cmake_configure_file")
 
 # Generates config.hh based on the version numbers in CMake code.
 cmake_configure_file(
diff --git a/tools/ipopt.BUILD b/tools/ipopt.BUILD
index f0d8942c7397..aeab83dc04ed 100644
--- a/tools/ipopt.BUILD
+++ b/tools/ipopt.BUILD
@@ -103,16 +103,16 @@ genrule(
     cmd = " ".join([
         "(",
         "env",
-        "cdexec=$(location @//tools/third_party/kythe/tools/cdexec:cdexec)",
+        "cdexec=$(location @kythe//tools/cdexec:cdexec)",
         "top_builddir=$(@D)",
-        "tools/ipopt_build_with_autotools.sh",
+        "$(location @drake//tools:ipopt_build_with_autotools.sh)",
         " 2>&1 > ipopt_build_with_autotools.log",
         ")",
         "|| (cat ipopt_build_with_autotools.log && false)",
     ]),
     tools = [
-        "@//tools:ipopt_build_with_autotools.sh",
-        "@//tools/third_party/kythe/tools/cdexec:cdexec",
+        "@drake//tools:ipopt_build_with_autotools.sh",
+        "@kythe//tools/cdexec:cdexec",
     ],
     visibility = ["//visibility:private"],
 )
diff --git a/tools/lcm.BUILD b/tools/lcm.BUILD
index 7fde6668f853..ea9556f742f9 100644
--- a/tools/lcm.BUILD
+++ b/tools/lcm.BUILD
@@ -1,9 +1,9 @@
 # -*- python -*-
 
-load("@//tools:drake.bzl", "drake_generate_file")
-load("@//tools:generate_export_header.bzl", "generate_export_header")
-load("@//tools:install.bzl", "install", "install_files")
-load("@//tools:python_lint.bzl", "python_lint")
+load("@drake//tools:drake.bzl", "drake_generate_file")
+load("@drake//tools:generate_export_header.bzl", "generate_export_header")
+load("@drake//tools:install.bzl", "install", "install_files")
+load("@drake//tools:python_lint.bzl", "python_lint")
 load("@bazel_tools//tools/build_defs/pkg:pkg.bzl", "pkg_tar")
 
 package(default_visibility = ["//visibility:public"])
@@ -200,8 +200,8 @@ pkg_tar(
 
 py_binary(
     name = "create-cps",
-    srcs = ["@//tools:lcm-create-cps.py"],
-    main = "@//tools:lcm-create-cps.py",
+    srcs = ["@drake//tools:lcm-create-cps.py"],
+    main = "@drake//tools:lcm-create-cps.py",
     visibility = ["//visibility:private"],
 )
 
diff --git a/tools/libbot.BUILD b/tools/libbot.BUILD
index 413237697c10..d027d395d85b 100644
--- a/tools/libbot.BUILD
+++ b/tools/libbot.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:lcm.bzl", "lcm_java_library", "lcm_py_library")
+load("@drake//tools:lcm.bzl", "lcm_java_library", "lcm_py_library")
 
 package(default_visibility = ["//visibility:public"])
 
diff --git a/tools/nlopt.BUILD b/tools/nlopt.BUILD
index a77c7c24acc3..48db4e8f78df 100644
--- a/tools/nlopt.BUILD
+++ b/tools/nlopt.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:cmake_configure_file.bzl", "cmake_configure_file")
+load("@drake//tools:cmake_configure_file.bzl", "cmake_configure_file")
 
 # Chooses the nlopt preprocessor substitutions that we want to use from Bazel.
 cmake_configure_file(
@@ -50,9 +50,9 @@ genrule(
         "api/nlopt.h",
     ],
     outs = ["api/nlopt.hpp"],
-    cmd = "$(location @//tools:nlopt-gen-hpp.sh) $(SRCS) $(OUTS) 2>&1 1>log" +
+    cmd = "$(location @drake//tools:nlopt-gen-hpp.sh) $(SRCS) $(OUTS) 2>&1 1>log" +
           " || (cat log && false)",
-    tools = ["@//tools:nlopt-gen-hpp.sh"],
+    tools = ["@drake//tools:nlopt-gen-hpp.sh"],
 )
 
 cc_library(
diff --git a/tools/robotlocomotion_lcmtypes.BUILD b/tools/robotlocomotion_lcmtypes.BUILD
index 6a22dffa2eec..e82a64b6bafa 100644
--- a/tools/robotlocomotion_lcmtypes.BUILD
+++ b/tools/robotlocomotion_lcmtypes.BUILD
@@ -2,7 +2,7 @@
 
 package(default_visibility = ["//visibility:public"])
 
-load("@//tools:lcm.bzl", "lcm_cc_library", "lcm_py_library")
+load("@drake//tools:lcm.bzl", "lcm_cc_library", "lcm_py_library")
 
 lcm_cc_library(
     name = "robotlocomotion_lcmtypes",
diff --git a/tools/sdformat.BUILD b/tools/sdformat.BUILD
index 5717e4ff7bee..587ff5d8036b 100644
--- a/tools/sdformat.BUILD
+++ b/tools/sdformat.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:cmake_configure_file.bzl", "cmake_configure_file")
+load("@drake//tools:cmake_configure_file.bzl", "cmake_configure_file")
 
 # Generates sdf_config.h based on the version numbers in CMake code.
 cmake_configure_file(
diff --git a/tools/semantic_version.BUILD b/tools/semantic_version.BUILD
index 2ed78c4aa39c..01a9c22b1bce 100644
--- a/tools/semantic_version.BUILD
+++ b/tools/semantic_version.BUILD
@@ -1,6 +1,6 @@
 # -*- python -*-
 
-load("@//tools:drake.bzl", "drake_generate_file")
+load("@drake//tools:drake.bzl", "drake_generate_file")
 
 py_library(
     name = "semantic_version",
diff --git a/tools/spdlog.BUILD b/tools/spdlog.BUILD
index 8f9180b369a3..d470c86c4e66 100644
--- a/tools/spdlog.BUILD
+++ b/tools/spdlog.BUILD
@@ -15,8 +15,8 @@ cc_library(
     ],
     includes = ["include"],
     linkopts = select({
-        "@//tools:linux": ["-pthread"],
-        "@//conditions:default": [],
+        "@drake//tools:linux": ["-pthread"],
+        "@//conditions:default": [],  # This is a bazel-default rule, and does not need @drake//
     }),
     deps = ["@fmt"],
 )
diff --git a/tools/third_party/kythe/WORKSPACE b/tools/third_party/kythe/WORKSPACE
new file mode 100644
index 000000000000..87ca36e82007
--- /dev/null
+++ b/tools/third_party/kythe/WORKSPACE
@@ -0,0 +1,6 @@
+# -*- python -*-
+
+# This file marks a workspace root for the Bazel build system. see
+# http://bazel.io/ .
+
+workspace(name = "kythe")
diff --git a/tools/third_party/kythe/tools/build_rules/config/local.bzl b/tools/third_party/kythe/tools/build_rules/config/local.bzl
index e75505ed4959..2e5e044aac89 100644
--- a/tools/third_party/kythe/tools/build_rules/config/local.bzl
+++ b/tools/third_party/kythe/tools/build_rules/config/local.bzl
@@ -50,7 +50,7 @@ local_cc_library_configure = repository_rule(
         "default": attr.string(),
         "defines": attr.string_list(),
         "build_file_template": attr.label(
-            default = Label("@//tools/third_party/kythe/tools/build_rules/config:BUILD.tpl"),
+            default = Label("@kythe//tools/build_rules/config:BUILD.tpl"),
             single_file = True,
             allow_files = True,
         ),
diff --git a/tools/third_party/kythe/tools/build_rules/config/pkg_config.bzl b/tools/third_party/kythe/tools/build_rules/config/pkg_config.bzl
index 18ad0085e474..063c81864f0e 100644
--- a/tools/third_party/kythe/tools/build_rules/config/pkg_config.bzl
+++ b/tools/third_party/kythe/tools/build_rules/config/pkg_config.bzl
@@ -174,7 +174,7 @@ pkg_config_package = repository_rule(
         "max_version": attr.string(),
         "exact_version": attr.string(),
         "build_file_template": attr.label(
-            default = Label("@//tools/third_party/kythe/tools/build_rules/config:BUILD.tpl"),
+            default = Label("@kythe//tools/build_rules/config:BUILD.tpl"),
             single_file = True,
             allow_files = True,
         ),
diff --git a/tools/third_party/kythe/tools/build_rules/config/system.bzl b/tools/third_party/kythe/tools/build_rules/config/system.bzl
index c793b66fac76..0003b8c7edfc 100644
--- a/tools/third_party/kythe/tools/build_rules/config/system.bzl
+++ b/tools/third_party/kythe/tools/build_rules/config/system.bzl
@@ -17,9 +17,9 @@ cc_system_package:
   repository, whose `:lib` target is then bound to '{name}'.
 """
 
-load("@//tools/third_party/kythe/tools/build_rules/config:wrapped_ctx.bzl", "wrapctx")
-load("@//tools/third_party/kythe/tools/build_rules/config:local.bzl", "setup_local_cc_library")
-load("@//tools/third_party/kythe/tools/build_rules/config:pkg_config.bzl", "setup_pkg_config_package")
+load("@kythe//tools/build_rules/config:wrapped_ctx.bzl", "wrapctx")
+load("@kythe//tools/build_rules/config:local.bzl", "setup_local_cc_library")
+load("@kythe//tools/build_rules/config:pkg_config.bzl", "setup_pkg_config_package")
 
 def try_local_library(repo_ctx):
   if repo_ctx.attr.envvar and repo_ctx.attr.envvar in repo_ctx.os.environ:
@@ -58,7 +58,7 @@ cc_system_package_configure = repository_rule(
         "default": attr.string(),
         "defines": attr.string_list(),
         "build_file_template": attr.label(
-            default = Label("@//tools/third_party/kythe/tools/build_rules/config:BUILD.tpl"),
+            default = Label("@kythe//tools/build_rules/config:BUILD.tpl"),
             single_file = True,
             allow_files = True,
         ),