diff --git a/internal/cli/format.go b/internal/cli/format.go
new file mode 100644
index 0000000..4e7e696
--- /dev/null
+++ b/internal/cli/format.go
@@ -0,0 +1,67 @@
+package cli
+
+import (
+	"context"
+	"fmt"
+	"io"
+	"os"
+
+	"github.com/deref/transcript/internal/core"
+	"github.com/natefinch/atomic"
+	"github.com/spf13/cobra"
+)
+
+func init() {
+	rootCmd.AddCommand(formatCmd)
+}
+
+var formatCmd = &cobra.Command{
+	Use:   "format [transcripts...]",
+	Short: "Formats transcript files",
+	Long: `Formats transcript files by normalizing comments, blank lines,
+trailing whitespace (except in command output), trailing newline,
+and special directive syntax.
+
+If no files are provided, reads from stdin and writes to stdout.
+If files are provided, formats them in-place.
+`,
+	RunE: func(cmd *cobra.Command, args []string) error {
+		ctx := cmd.Context()
+		if len(args) == 0 {
+			// Read from stdin, write to stdout
+			return formatStdin(ctx)
+		}
+		// Format files in-place
+		for _, filename := range args {
+			if err := formatFile(ctx, filename); err != nil {
+				return fmt.Errorf("formatting %q: %w", filename, err)
+			}
+		}
+		return nil
+	},
+}
+
+func formatStdin(ctx context.Context) error {
+	formatter := &core.Formatter{}
+	transcript, err := formatter.FormatTranscript(ctx, os.Stdin)
+	if err != nil {
+		return err
+	}
+	_, err = io.Copy(os.Stdout, transcript)
+	return err
+}
+
+func formatFile(ctx context.Context, filename string) error {
+	f, err := os.Open(filename)
+	if err != nil {
+		return err
+	}
+	defer f.Close()
+
+	formatter := &core.Formatter{}
+	transcript, err := formatter.FormatTranscript(ctx, f)
+	if err != nil {
+		return err
+	}
+	return atomic.WriteFile(filename, transcript)
+}
diff --git a/internal/core/formatter.go b/internal/core/formatter.go
new file mode 100644
index 0000000..34c7d1f
--- /dev/null
+++ b/internal/core/formatter.go
@@ -0,0 +1,94 @@
+package core
+
+import (
+	"bytes"
+	"context"
+	"io"
+	"strconv"
+	"strings"
+)
+
+type Formatter struct {
+	buf *bytes.Buffer
+}
+
+func (f *Formatter) FormatTranscript(ctx context.Context, r io.Reader) (transcript *bytes.Buffer, err error) {
+	f.buf = &bytes.Buffer{}
+
+	// Use the regular interpreter with the formatter as handler.
+	interp := &Interpreter{
+		Handler: f,
+	}
+	if err := interp.ExecTranscript(ctx, r); err != nil {
+		return nil, err
+	}
+
+	// Ensure file ends with exactly one newline
+	content := f.buf.Bytes()
+	content = bytes.TrimRight(content, "\n")
+	if len(content) > 0 {
+		content = append(content, '\n')
+	}
+
+	return bytes.NewBuffer(content), nil
+}
+
+func (f *Formatter) HandleComment(ctx context.Context, text string) error {
+	// Normalize comments and blank lines
+	trimmed := strings.TrimSpace(text)
+	if trimmed == "" {
+		// Blank line
+		f.buf.WriteString("\n")
+	} else if strings.HasPrefix(trimmed, "#") {
+		// Normalize comment formatting
+		comment := strings.TrimPrefix(trimmed, "#")
+		comment = strings.TrimSpace(comment)
+		if comment == "" {
+			f.buf.WriteString("#\n")
+		} else {
+			f.buf.WriteString("# " + comment + "\n")
+		}
+	}
+
+	return nil
+}
+
+func (f *Formatter) HandleRun(ctx context.Context, command string) error {
+	// Write the command with normalized formatting
+	f.buf.WriteString("$ " + strings.TrimSpace(command) + "\n")
+
+	return nil
+}
+
+func (f *Formatter) HandleOutput(ctx context.Context, fd int, line string) error {
+	// Output lines preserve their exact content (including whitespace)
+	f.buf.WriteString(strconv.Itoa(fd) + " " + line + "\n")
+
+	return nil
+}
+
+func (f *Formatter) HandleFileOutput(ctx context.Context, fd int, filepath string) error {
+	// File output references with normalized formatting
+	f.buf.WriteString(strconv.Itoa(fd) + "< " + strings.TrimSpace(filepath) + "\n")
+
+	return nil
+}
+
+func (f *Formatter) HandleNoNewline(ctx context.Context, fd int) error {
+	// No-newline directive with normalized formatting
+	f.buf.WriteString("% no-newline\n")
+
+	return nil
+}
+
+func (f *Formatter) HandleExitCode(ctx context.Context, exitCode int) error {
+	// Exit code with normalized formatting
+	f.buf.WriteString("? " + strconv.Itoa(exitCode) + "\n")
+
+	return nil
+}
+
+func (f *Formatter) HandleEnd(ctx context.Context) error {
+	// No special handling needed for end
+	return nil
+}
diff --git a/internal/core/updater.go b/internal/core/updater.go
index f3feac3..2397105 100644
--- a/internal/core/updater.go
+++ b/internal/core/updater.go
@@ -35,19 +35,19 @@ func (upr *Updater) flushCurrentCommand(ctx context.Context) error {
 	if upr.currentCommand == "" {
 		return nil // No command to flush
 	}
-	
+
 	// Set up recorder with file references for this command
 	upr.rec.SetPreferredFiles(upr.fileRefs)
-	
+
 	// Execute the command
 	if _, err := upr.rec.RunCommand(ctx, upr.currentCommand); err != nil {
 		return err
 	}
-	
+
 	// Clear the buffer
 	upr.fileRefs = nil
 	upr.currentCommand = ""
-	
+
 	return nil
 }
 
@@ -66,7 +66,7 @@ func (upr *Updater) HandleRun(ctx context.Context, command string) error {
 	if err := upr.flushCurrentCommand(ctx); err != nil {
 		return err
 	}
-	
+
 	// Buffer this command - don't execute it yet
 	upr.currentCommand = command
 	return nil
@@ -97,4 +97,3 @@ func (upr *Updater) HandleEnd(ctx context.Context) error {
 	// Flush any remaining command at the end
 	return upr.flushCurrentCommand(ctx)
 }
-
diff --git a/tests/format-basic.cmdt b/tests/format-basic.cmdt
new file mode 100644
index 0000000..4ecaabc
--- /dev/null
+++ b/tests/format-basic.cmdt
@@ -0,0 +1,14 @@
+# Test basic formatting
+
+$ echo hello
+1 hello
+
+# Multiple blank lines should be normalized
+
+
+$ echo world 
+1 world
+
+   # Comment with irregular spacing
+$ false
+? 1
\ No newline at end of file
diff --git a/tests/format-basic.cmdt.expected b/tests/format-basic.cmdt.expected
new file mode 100644
index 0000000..68b64ee
--- /dev/null
+++ b/tests/format-basic.cmdt.expected
@@ -0,0 +1,13 @@
+# Test basic formatting
+
+$ echo hello
+1 hello
+
+# Multiple blank lines should be normalized
+
+$ echo world
+1 world
+
+# Comment with irregular spacing
+$ false
+? 1
\ No newline at end of file
diff --git a/tests/format-command.cmdt b/tests/format-command.cmdt
new file mode 100644
index 0000000..16f55f5
--- /dev/null
+++ b/tests/format-command.cmdt
@@ -0,0 +1,42 @@
+# Test format command functionality
+
+# Create a file with formatting issues
+$ cat > unformatted.cmdt <<'EOF'
+#comment without space
+
+
+$ echo hello 
+1 hello
+
+   # irregular comment spacing
+$ false   
+? 1  
+EOF
+
+# Test stdin/stdout formatting
+$ transcript format < unformatted.cmdt
+1 # comment without space
+1 
+1 $ echo hello
+1 1 hello
+1 
+1 # irregular comment spacing
+1 $ false
+1 ? 1
+
+# Test actual formatting (in-place)
+$ transcript format unformatted.cmdt
+
+# Verify the file was formatted correctly
+$ cat unformatted.cmdt
+1 # comment without space
+1 
+1 $ echo hello
+1 1 hello
+1 
+1 # irregular comment spacing
+1 $ false
+1 ? 1
+
+# Clean up
+$ rm unformatted.cmdt
\ No newline at end of file
diff --git a/tests/format-simple.cmdt b/tests/format-simple.cmdt
new file mode 100644
index 0000000..d759eee
--- /dev/null
+++ b/tests/format-simple.cmdt
@@ -0,0 +1,21 @@
+# Test simple format command
+
+# Create a file with whitespace and formatting issues
+$ cat > test.cmdt <<'EOF'
+#comment
+$ echo test   
+1 test
+   #another comment   
+? 0
+EOF
+
+# Format it using stdin/stdout
+$ transcript format < test.cmdt
+1 # comment
+1 $ echo test
+1 1 test
+1 # another comment
+1 ? 0
+
+# Clean up
+$ rm test.cmdt
\ No newline at end of file