diff --git a/pkg/transport/stdio.go b/pkg/transport/stdio.go
index f774d36..de433e2 100644
--- a/pkg/transport/stdio.go
+++ b/pkg/transport/stdio.go
@@ -1,6 +1,7 @@
 package transport
 
 import (
+	"bufio"
 	"bytes"
 	"encoding/json"
 	"fmt"
@@ -31,12 +32,27 @@ func NewStdio(command []string) *Stdio {
 // Execute implements the Transport interface by spawning a subprocess
 // and communicating with it via JSON-RPC over stdin/stdout.
 func (t *Stdio) Execute(method string, params any) (map[string]any, error) {
-	if len(t.command) == 0 {
-		return nil, fmt.Errorf("no command specified for stdio transport")
+	stdin, stdout, cmd, stderrBuf, err := t.setupCommand()
+	if err != nil {
+		return nil, err
 	}
 
 	if t.debug {
-		fmt.Fprintf(os.Stderr, "DEBUG: Executing command: %v\n", t.command)
+		fmt.Fprintf(os.Stderr, "DEBUG: Starting initialization\n")
+	}
+
+	if initErr := t.initialize(stdin, stdout); initErr != nil {
+		if t.debug {
+			fmt.Fprintf(os.Stderr, "DEBUG: Initialization failed: %v\n", initErr)
+			if stderrBuf.Len() > 0 {
+				fmt.Fprintf(os.Stderr, "DEBUG: stderr during init: %s\n", stderrBuf.String())
+			}
+		}
+		return nil, initErr
+	}
+
+	if t.debug {
+		fmt.Fprintf(os.Stderr, "DEBUG: Initialization successful, sending method request\n")
 	}
 
 	request := Request{
@@ -47,77 +63,155 @@ func (t *Stdio) Execute(method string, params any) (map[string]any, error) {
 	}
 	t.nextID++
 
-	requestJSON, err := json.Marshal(request)
+	if sendErr := t.sendRequest(stdin, request); sendErr != nil {
+		return nil, sendErr
+	}
+	_ = stdin.Close()
+
+	response, err := t.readResponse(stdout)
 	if err != nil {
-		return nil, fmt.Errorf("error marshaling request: %w", err)
+		return nil, err
 	}
 
-	requestJSON = append(requestJSON, '\n')
+	waitErr := cmd.Wait()
 
 	if t.debug {
-		fmt.Fprintf(os.Stderr, "DEBUG: Sending request: %s\n", string(requestJSON))
+		fmt.Fprintf(os.Stderr, "DEBUG: Command completed with err: %v\n", waitErr)
+		if stderrBuf.Len() > 0 {
+			fmt.Fprintf(os.Stderr, "DEBUG: stderr output:\n%s\n", stderrBuf.String())
+		}
 	}
 
-	cmd := exec.Command(t.command[0], t.command[1:]...) // #nosec G204
+	if waitErr != nil && stderrBuf.Len() > 0 {
+		return nil, fmt.Errorf("command error: %w, stderr: %s", waitErr, stderrBuf.String())
+	}
+
+	return response.Result, nil
+}
 
-	stdin, stdinErr := cmd.StdinPipe()
-	if stdinErr != nil {
-		return nil, fmt.Errorf("error getting stdin pipe: %w", stdinErr)
+// setupCommand prepares and starts the command, returning the stdin/stdout pipes and any error.
+func (t *Stdio) setupCommand() (stdin io.WriteCloser, stdout io.ReadCloser, cmd *exec.Cmd, stderrBuf *bytes.Buffer, err error) {
+	if len(t.command) == 0 {
+		return nil, nil, nil, nil, fmt.Errorf("no command specified for stdio transport")
 	}
 
-	stdout, stdoutErr := cmd.StdoutPipe()
-	if stdoutErr != nil {
-		return nil, fmt.Errorf("error getting stdout pipe: %w", stdoutErr)
+	if t.debug {
+		fmt.Fprintf(os.Stderr, "DEBUG: Executing command: %v\n", t.command)
 	}
 
-	var stderrBuf bytes.Buffer
-	cmd.Stderr = &stderrBuf
+	cmd = exec.Command(t.command[0], t.command[1:]...) // #nosec G204
+
+	stdin, err = cmd.StdinPipe()
+	if err != nil {
+		return nil, nil, nil, nil, fmt.Errorf("error getting stdin pipe: %w", err)
+	}
 
-	if startErr := cmd.Start(); startErr != nil {
-		return nil, fmt.Errorf("error starting command: %w", startErr)
+	stdout, err = cmd.StdoutPipe()
+	if err != nil {
+		return nil, nil, nil, nil, fmt.Errorf("error getting stdout pipe: %w", err)
 	}
 
-	if _, writeErr := stdin.Write(requestJSON); writeErr != nil {
-		return nil, fmt.Errorf("error writing to stdin: %w", writeErr)
+	stderrBuf = &bytes.Buffer{}
+	cmd.Stderr = stderrBuf
+
+	if err = cmd.Start(); err != nil {
+		return nil, nil, nil, nil, fmt.Errorf("error starting command: %w", err)
+	}
+
+	return stdin, stdout, cmd, stderrBuf, nil
+}
+
+// initialize sends the initialization request and waits for response and then sends the initialized
+// notification.
+func (t *Stdio) initialize(stdin io.WriteCloser, stdout io.ReadCloser) error {
+	initRequest := Request{
+		JSONRPC: "2.0",
+		Method:  "initialize",
+		ID:      t.nextID,
+		Params: map[string]any{
+			"clientInfo": map[string]any{
+				"name":    "f/mcptools",
+				"version": "beta",
+			},
+			"protocolVersion": protocolVersion,
+			"capabilities":    map[string]any{},
+		},
+	}
+	t.nextID++
+
+	if err := t.sendRequest(stdin, initRequest); err != nil {
+		return fmt.Errorf("init request failed: %w", err)
 	}
-	_ = stdin.Close()
+
+	_, err := t.readResponse(stdout)
+	if err != nil {
+		return fmt.Errorf("init response failed: %w", err)
+	}
+
+	initNotification := Request{
+		JSONRPC: "2.0",
+		Method:  "notifications/initialized",
+	}
+
+	if sendErr := t.sendRequest(stdin, initNotification); sendErr != nil {
+		return fmt.Errorf("init notification failed: %w", sendErr)
+	}
+
+	return nil
+}
+
+// sendRequest sends a JSON-RPC request and returns the marshaled request.
+func (t *Stdio) sendRequest(stdin io.WriteCloser, request Request) error {
+	requestJSON, err := json.Marshal(request)
+	if err != nil {
+		return fmt.Errorf("error marshaling request: %w", err)
+	}
+	requestJSON = append(requestJSON, '\n')
 
 	if t.debug {
-		fmt.Fprintf(os.Stderr, "DEBUG: Wrote request to stdin\n")
+		fmt.Fprintf(os.Stderr, "DEBUG: Preparing to send request: %s\n", string(requestJSON))
 	}
 
-	var respBytes bytes.Buffer
-	if _, copyErr := io.Copy(&respBytes, stdout); copyErr != nil {
-		return nil, fmt.Errorf("error reading from stdout: %w", copyErr)
+	writer := bufio.NewWriter(stdin)
+	n, err := writer.Write(requestJSON)
+	if err != nil {
+		return fmt.Errorf("error writing bytes to stdin: %w", err)
 	}
 
 	if t.debug {
-		fmt.Fprintf(os.Stderr, "DEBUG: Read from stdout: %s\n", respBytes.String())
+		fmt.Fprintf(os.Stderr, "DEBUG: Wrote %d bytes\n", n)
 	}
 
-	waitErr := cmd.Wait()
+	if flushErr := writer.Flush(); flushErr != nil {
+		return fmt.Errorf("error flushing bytes to stdin: %w", flushErr)
+	}
 
 	if t.debug {
-		fmt.Fprintf(os.Stderr, "DEBUG: Command completed with err: %v\n", waitErr)
-		if stderrBuf.Len() > 0 {
-			fmt.Fprintf(os.Stderr, "DEBUG: stderr output: %s\n", stderrBuf.String())
-		}
+		fmt.Fprintf(os.Stderr, "DEBUG: Successfully flushed bytes\n")
 	}
 
-	if waitErr != nil && stderrBuf.Len() > 0 {
-		return nil, fmt.Errorf("command error: %w, stderr: %s", waitErr, stderrBuf.String())
+	return nil
+}
+
+// readResponse reads and parses a JSON-RPC response.
+func (t *Stdio) readResponse(stdout io.ReadCloser) (*Response, error) {
+	reader := bufio.NewReader(stdout)
+	line, err := reader.ReadBytes('\n')
+	if err != nil {
+		return nil, fmt.Errorf("error reading from stdout: %w", err)
 	}
 
-	if respBytes.Len() == 0 {
-		if stderrBuf.Len() > 0 {
-			return nil, fmt.Errorf("no response from command, stderr: %s", stderrBuf.String())
-		}
+	if t.debug {
+		fmt.Fprintf(os.Stderr, "DEBUG: Read from stdout: %s", string(line))
+	}
+
+	if len(line) == 0 {
 		return nil, fmt.Errorf("no response from command")
 	}
 
 	var response Response
-	if unmarshalErr := json.Unmarshal(respBytes.Bytes(), &response); unmarshalErr != nil {
-		return nil, fmt.Errorf("error unmarshaling response: %w, response: %s", unmarshalErr, respBytes.String())
+	if unmarshalErr := json.Unmarshal(line, &response); unmarshalErr != nil {
+		return nil, fmt.Errorf("error unmarshaling response: %w, response: %s", unmarshalErr, string(line))
 	}
 
 	if response.Error != nil {
@@ -128,5 +222,5 @@ func (t *Stdio) Execute(method string, params any) (map[string]any, error) {
 		fmt.Fprintf(os.Stderr, "DEBUG: Successfully parsed response\n")
 	}
 
-	return response.Result, nil
+	return &response, nil
 }
diff --git a/pkg/transport/transport.go b/pkg/transport/transport.go
index 6341aab..b27b7a8 100644
--- a/pkg/transport/transport.go
+++ b/pkg/transport/transport.go
@@ -6,6 +6,10 @@ import (
 	"io"
 )
 
+const (
+	protocolVersion = "2024-11-05"
+)
+
 // Transport defines the interface for communicating with MCP servers.
 // Implementations should handle the specifics of communication protocols.
 type Transport interface {
@@ -17,7 +21,7 @@ type Request struct {
 	Params  any    `json:"params,omitempty"`
 	JSONRPC string `json:"jsonrpc"`
 	Method  string `json:"method"`
-	ID      int    `json:"id"`
+	ID      int    `json:"id,omitempty"`
 }
 
 // Response represents a JSON-RPC 2.0 response.