diff --git a/README.md b/README.md
index 6c4c5279..2acf2fd5 100644
--- a/README.md
+++ b/README.md
@@ -86,7 +86,7 @@ If you want to build a local command-line application, you can use the stdio tra
 ```ruby
 #!/usr/bin/env ruby
 require "mcp"
-require "mcp/transports/stdio"
+require "mcp/server/transports/stdio"
 
 # Create a simple tool
 class ExampleTool < MCP::Tool
@@ -115,7 +115,7 @@ server = MCP::Server.new(
 )
 
 # Create and start the transport
-transport = MCP::Transports::StdioTransport.new(server)
+transport = MCP::Server::Transports::StdioTransport.new(server)
 transport.open
 ```
 
diff --git a/examples/stdio_server.rb b/examples/stdio_server.rb
index 177b3721..cddf912e 100755
--- a/examples/stdio_server.rb
+++ b/examples/stdio_server.rb
@@ -3,7 +3,7 @@
 
 $LOAD_PATH.unshift(File.expand_path("../lib", __dir__))
 require "mcp"
-require "mcp/transports/stdio"
+require "mcp/server/transports/stdio"
 
 # Create a simple tool
 class ExampleTool < MCP::Tool
@@ -91,5 +91,5 @@ def template(args, server_context:)
 end
 
 # Create and start the transport
-transport = MCP::Transports::StdioTransport.new(server)
+transport = MCP::Server::Transports::StdioTransport.new(server)
 transport.open
diff --git a/lib/mcp.rb b/lib/mcp.rb
index 7eb8870a..cb2c2f92 100644
--- a/lib/mcp.rb
+++ b/lib/mcp.rb
@@ -1,23 +1,26 @@
 # frozen_string_literal: true
 
-require_relative "mcp/server"
-require_relative "mcp/string_utils"
-require_relative "mcp/tool"
-require_relative "mcp/tool/input_schema"
-require_relative "mcp/tool/annotations"
-require_relative "mcp/tool/response"
+require_relative "mcp/configuration"
 require_relative "mcp/content"
-require_relative "mcp/resource"
-require_relative "mcp/resource/contents"
-require_relative "mcp/resource/embedded"
-require_relative "mcp/resource_template"
+require_relative "mcp/instrumentation"
+require_relative "mcp/methods"
 require_relative "mcp/prompt"
 require_relative "mcp/prompt/argument"
 require_relative "mcp/prompt/message"
 require_relative "mcp/prompt/result"
+require_relative "mcp/resource"
+require_relative "mcp/resource/contents"
+require_relative "mcp/resource/embedded"
+require_relative "mcp/resource_template"
+require_relative "mcp/server"
+require_relative "mcp/server/transports/stdio"
+require_relative "mcp/string_utils"
+require_relative "mcp/tool"
+require_relative "mcp/tool/input_schema"
+require_relative "mcp/tool/response"
+require_relative "mcp/tool/annotations"
+require_relative "mcp/transport"
 require_relative "mcp/version"
-require_relative "mcp/configuration"
-require_relative "mcp/methods"
 
 module MCP
   class << self
diff --git a/lib/mcp/server/transports/stdio.rb b/lib/mcp/server/transports/stdio.rb
new file mode 100644
index 00000000..a90ea67d
--- /dev/null
+++ b/lib/mcp/server/transports/stdio.rb
@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+require_relative "../../transport"
+require "json"
+
+module MCP
+  class Server
+    module Transports
+      class StdioTransport < Transport
+        def initialize(server)
+          @server = server
+          @open = false
+          $stdin.set_encoding("UTF-8")
+          $stdout.set_encoding("UTF-8")
+          super
+        end
+
+        def open
+          @open = true
+          while @open && (line = $stdin.gets)
+            handle_json_request(line.strip)
+          end
+        end
+
+        def close
+          @open = false
+        end
+
+        def send_response(message)
+          json_message = message.is_a?(String) ? message : JSON.generate(message)
+          $stdout.puts(json_message)
+          $stdout.flush
+        end
+      end
+    end
+  end
+end
diff --git a/lib/mcp/transports/stdio.rb b/lib/mcp/transports/stdio.rb
deleted file mode 100644
index b76b9619..00000000
--- a/lib/mcp/transports/stdio.rb
+++ /dev/null
@@ -1,35 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../transport"
-require "json"
-
-module MCP
-  module Transports
-    class StdioTransport < Transport
-      def initialize(server)
-        @server = server
-        @open = false
-        $stdin.set_encoding("UTF-8")
-        $stdout.set_encoding("UTF-8")
-        super
-      end
-
-      def open
-        @open = true
-        while @open && (line = $stdin.gets)
-          handle_json_request(line.strip)
-        end
-      end
-
-      def close
-        @open = false
-      end
-
-      def send_response(message)
-        json_message = message.is_a?(String) ? message : JSON.generate(message)
-        $stdout.puts(json_message)
-        $stdout.flush
-      end
-    end
-  end
-end
diff --git a/test/model_context_protocol/configuration_test.rb b/test/mcp/configuration_test.rb
similarity index 100%
rename from test/model_context_protocol/configuration_test.rb
rename to test/mcp/configuration_test.rb
diff --git a/test/model_context_protocol/instrumentation_test.rb b/test/mcp/instrumentation_test.rb
similarity index 100%
rename from test/model_context_protocol/instrumentation_test.rb
rename to test/mcp/instrumentation_test.rb
diff --git a/test/model_context_protocol/methods_test.rb b/test/mcp/methods_test.rb
similarity index 100%
rename from test/model_context_protocol/methods_test.rb
rename to test/mcp/methods_test.rb
diff --git a/test/model_context_protocol/prompt_test.rb b/test/mcp/prompt_test.rb
similarity index 100%
rename from test/model_context_protocol/prompt_test.rb
rename to test/mcp/prompt_test.rb
diff --git a/test/mcp/server/transports/stdio_test.rb b/test/mcp/server/transports/stdio_test.rb
new file mode 100644
index 00000000..57a16909
--- /dev/null
+++ b/test/mcp/server/transports/stdio_test.rb
@@ -0,0 +1,127 @@
+# frozen_string_literal: true
+
+require "test_helper"
+require "mcp/server/transports/stdio"
+require "json"
+
+module MCP
+  class Server
+    module Transports
+      class StdioTest < ActiveSupport::TestCase
+        include InstrumentationTestHelper
+
+        setup do
+          configuration = MCP::Configuration.new
+          configuration.instrumentation_callback = instrumentation_helper.callback
+          @server = Server.new(name: "test_server", configuration: configuration)
+          @transport = StdioTransport.new(@server)
+        end
+
+        test "initializes with server and closed state" do
+          server = @transport.instance_variable_get(:@server)
+          assert_equal @server.object_id, server.object_id
+          refute @transport.instance_variable_get(:@open)
+        end
+
+        test "processes JSON-RPC requests from stdin and sends responses to stdout" do
+          request = {
+            jsonrpc: "2.0",
+            method: "ping",
+            id: "123",
+          }
+          input = StringIO.new(JSON.generate(request) + "\n")
+          output = StringIO.new
+
+          original_stdin = $stdin
+          original_stdout = $stdout
+
+          begin
+            $stdin = input
+            $stdout = output
+
+            thread = Thread.new { @transport.open }
+            sleep(0.1)
+            @transport.close
+            thread.join
+
+            response = JSON.parse(output.string, symbolize_names: true)
+            assert_equal("2.0", response[:jsonrpc])
+            assert_equal("123", response[:id])
+            assert_empty(response[:result])
+            refute(@transport.instance_variable_get(:@open))
+          ensure
+            $stdin = original_stdin
+            $stdout = original_stdout
+          end
+        end
+
+        test "sends string responses to stdout" do
+          output = StringIO.new
+          original_stdout = $stdout
+
+          begin
+            $stdout = output
+            @transport.send_response("test response")
+            assert_equal("test response\n", output.string)
+          ensure
+            $stdout = original_stdout
+          end
+        end
+
+        test "sends JSON responses to stdout" do
+          output = StringIO.new
+          original_stdout = $stdout
+
+          begin
+            $stdout = output
+            response = { key: "value" }
+            @transport.send_response(response)
+            assert_equal(JSON.generate(response) + "\n", output.string)
+          ensure
+            $stdout = original_stdout
+          end
+        end
+
+        test "handles valid JSON-RPC requests" do
+          request = {
+            jsonrpc: "2.0",
+            method: "ping",
+            id: "123",
+          }
+          output = StringIO.new
+          original_stdout = $stdout
+
+          begin
+            $stdout = output
+            @transport.send(:handle_request, JSON.generate(request))
+            response = JSON.parse(output.string, symbolize_names: true)
+            assert_equal("2.0", response[:jsonrpc])
+            assert_nil(response[:id])
+            assert_nil(response[:result])
+          ensure
+            $stdout = original_stdout
+          end
+        end
+
+        test "handles invalid JSON requests" do
+          invalid_json = "invalid json"
+          output = StringIO.new
+          original_stdout = $stdout
+
+          begin
+            $stdout = output
+            @transport.send(:handle_request, invalid_json)
+            response = JSON.parse(output.string, symbolize_names: true)
+            assert_equal("2.0", response[:jsonrpc])
+            assert_nil(response[:id])
+            assert_equal(-32600, response[:error][:code])
+            assert_equal("Invalid Request", response[:error][:message])
+            assert_equal("Request must be an array or a hash", response[:error][:data])
+          ensure
+            $stdout = original_stdout
+          end
+        end
+      end
+    end
+  end
+end
diff --git a/test/model_context_protocol/server_test.rb b/test/mcp/server_test.rb
similarity index 100%
rename from test/model_context_protocol/server_test.rb
rename to test/mcp/server_test.rb
diff --git a/test/model_context_protocol/string_utils_test.rb b/test/mcp/string_utils_test.rb
similarity index 100%
rename from test/model_context_protocol/string_utils_test.rb
rename to test/mcp/string_utils_test.rb
diff --git a/test/model_context_protocol/tool/input_schema_test.rb b/test/mcp/tool/input_schema_test.rb
similarity index 100%
rename from test/model_context_protocol/tool/input_schema_test.rb
rename to test/mcp/tool/input_schema_test.rb
diff --git a/test/model_context_protocol/tool_test.rb b/test/mcp/tool_test.rb
similarity index 100%
rename from test/model_context_protocol/tool_test.rb
rename to test/mcp/tool_test.rb
diff --git a/test/model_context_protocol/transports/stdio_transport_test.rb b/test/model_context_protocol/transports/stdio_transport_test.rb
deleted file mode 100644
index 2fe5df2a..00000000
--- a/test/model_context_protocol/transports/stdio_transport_test.rb
+++ /dev/null
@@ -1,125 +0,0 @@
-# frozen_string_literal: true
-
-require "test_helper"
-require "mcp/transports/stdio"
-require "json"
-
-module MCP
-  module Transports
-    class StdioTransportTest < ActiveSupport::TestCase
-      include InstrumentationTestHelper
-
-      setup do
-        configuration = MCP::Configuration.new
-        configuration.instrumentation_callback = instrumentation_helper.callback
-        @server = Server.new(name: "test_server", configuration: configuration)
-        @transport = StdioTransport.new(@server)
-      end
-
-      test "initializes with server and closed state" do
-        server = @transport.instance_variable_get(:@server)
-        assert_equal @server.object_id, server.object_id
-        refute @transport.instance_variable_get(:@open)
-      end
-
-      test "processes JSON-RPC requests from stdin and sends responses to stdout" do
-        request = {
-          jsonrpc: "2.0",
-          method: "ping",
-          id: "123",
-        }
-        input = StringIO.new(JSON.generate(request) + "\n")
-        output = StringIO.new
-
-        original_stdin = $stdin
-        original_stdout = $stdout
-
-        begin
-          $stdin = input
-          $stdout = output
-
-          thread = Thread.new { @transport.open }
-          sleep(0.1)
-          @transport.close
-          thread.join
-
-          response = JSON.parse(output.string, symbolize_names: true)
-          assert_equal("2.0", response[:jsonrpc])
-          assert_equal("123", response[:id])
-          assert_empty(response[:result])
-          refute(@transport.instance_variable_get(:@open))
-        ensure
-          $stdin = original_stdin
-          $stdout = original_stdout
-        end
-      end
-
-      test "sends string responses to stdout" do
-        output = StringIO.new
-        original_stdout = $stdout
-
-        begin
-          $stdout = output
-          @transport.send_response("test response")
-          assert_equal("test response\n", output.string)
-        ensure
-          $stdout = original_stdout
-        end
-      end
-
-      test "sends JSON responses to stdout" do
-        output = StringIO.new
-        original_stdout = $stdout
-
-        begin
-          $stdout = output
-          response = { key: "value" }
-          @transport.send_response(response)
-          assert_equal(JSON.generate(response) + "\n", output.string)
-        ensure
-          $stdout = original_stdout
-        end
-      end
-
-      test "handles valid JSON-RPC requests" do
-        request = {
-          jsonrpc: "2.0",
-          method: "ping",
-          id: "123",
-        }
-        output = StringIO.new
-        original_stdout = $stdout
-
-        begin
-          $stdout = output
-          @transport.send(:handle_request, JSON.generate(request))
-          response = JSON.parse(output.string, symbolize_names: true)
-          assert_equal("2.0", response[:jsonrpc])
-          assert_nil(response[:id])
-          assert_nil(response[:result])
-        ensure
-          $stdout = original_stdout
-        end
-      end
-
-      test "handles invalid JSON requests" do
-        invalid_json = "invalid json"
-        output = StringIO.new
-        original_stdout = $stdout
-
-        begin
-          $stdout = output
-          @transport.send(:handle_request, invalid_json)
-          response = JSON.parse(output.string, symbolize_names: true)
-          assert_equal("2.0", response[:jsonrpc])
-          assert_nil(response[:id])
-          assert_equal(-32600, response[:error][:code])
-          assert_equal("Invalid Request", response[:error][:message])
-          assert_equal("Request must be an array or a hash", response[:error][:data])
-        ensure
-          $stdout = original_stdout
-        end
-      end
-    end
-  end
-end