diff --git a/patchwork/steps/ModifyCode/ModifyCode.py b/patchwork/steps/ModifyCode/ModifyCode.py
index f7c6d7e4f..4bc2003cd 100644
--- a/patchwork/steps/ModifyCode/ModifyCode.py
+++ b/patchwork/steps/ModifyCode/ModifyCode.py
@@ -1,23 +1,48 @@
 from __future__ import annotations
 
 from pathlib import Path
+from typing import Union, List
 
 from patchwork.step import Step, StepStatus
 
 
-def save_file_contents(file_path, content):
-    """Utility function to save content to a file."""
-    with open(file_path, "w") as file:
+def save_file_contents(file_path: str, content: Union[str, bytes]) -> None:
+    """Utility function to save content to a file in binary mode to preserve line endings.
+    
+    Args:
+        file_path: Path to the file to write
+        content: Content to write, either as string or bytes. If string, it will be encoded as UTF-8."""
+    with open(file_path, "wb") as file:
+        # Convert string to bytes if needed
+        if isinstance(content, str):
+            content = content.encode('utf-8')
         file.write(content)
 
 
-def handle_indent(src: list[str], target: list[str], start: int, end: int) -> list[str]:
+def handle_indent(src: List[str], target: List[str], start: int, end: int) -> List[str]:
+    """Handles indentation of new code to match the original code's indentation level.
+    
+    Args:
+        src: Source lines from the original file
+        target: New lines that need to be indented
+        start: Start line number in the source file
+        end: End line number in the source file
+    
+    Returns:
+        List of strings with proper indentation applied
+    
+    Note:
+        - If target is empty, returns it as is
+        - If start equals end, uses start + 1 as end to ensure at least one line
+        - Preserves existing indentation characters (spaces or tabs)
+    """
     if len(target) < 1:
         return target
 
     if start == end:
         end = start + 1
 
+    # Find first non-empty line in source and target
     first_src_line = next((line for line in src[start:end] if line.strip() != ""), "")
     src_indent_count = len(first_src_line) - len(first_src_line.lstrip())
     first_target_line = next((line for line in target if line.strip() != ""), "")
@@ -26,36 +51,101 @@ def handle_indent(src: list[str], target: list[str], start: int, end: int) -> li
 
     indent = ""
     if indent_diff > 0:
+        # Use the same indentation character as the source (space or tab)
         indent_unit = first_src_line[0]
         indent = indent_unit * indent_diff
 
     return [indent + line for line in target]
 
 
+def detect_line_ending(content: bytes) -> bytes:
+    """Detect the dominant line ending style in the given bytes content.
+    
+    Args:
+        content: File content in bytes to analyze
+        
+    Returns:
+        The detected line ending as bytes (b'\\r\\n', b'\\n', or b'\\r')
+        
+    Note:
+        - Counts occurrences of different line endings (CRLF, LF, CR)
+        - Returns the most common line ending
+        - Handles cases where \r\n is treated as one ending, not two
+        - Defaults to \\n if no line endings are found"""
+    crlf_count = content.count(b'\r\n')
+    lf_count = content.count(b'\n') - crlf_count  # Don't count \n that are part of \r\n
+    cr_count = content.count(b'\r') - crlf_count  # Don't count \r that are part of \r\n
+    
+    if crlf_count > max(lf_count, cr_count):
+        return b'\r\n'
+    elif lf_count > cr_count:
+        return b'\n'
+    elif cr_count > 0:
+        return b'\r'
+    return b'\n'  # Default to \n if no line endings found
+
 def replace_code_in_file(
     file_path: str,
-    start_line: int | None,
-    end_line: int | None,
+    start_line: Union[int, None],
+    end_line: Union[int, None],
     new_code: str,
 ) -> None:
+    """Replace specified lines in a file with new code while preserving line endings.
+
+    Args:
+        file_path: Path to the file to modify
+        start_line: Starting line number for replacement (0-based). If None, writes entire file
+        end_line: Ending line number for replacement (0-based). If None, writes entire file
+        new_code: New content to insert
+
+    Note:
+        - Preserves the original file's line ending style (CRLF, LF, or CR)
+        - Handles indentation to match the original code
+        - Creates new file if it doesn't exist
+        - Uses system default line ending for new files
+        - Ensures all lines end with proper line ending
+        - Preserves UTF-8 encoding
+    """
     path = Path(file_path)
+    
+    # Convert new_code to use \n for initial splitting
     new_code_lines = new_code.splitlines(keepends=True)
     if len(new_code_lines) > 0 and not new_code_lines[-1].endswith("\n"):
         new_code_lines[-1] += "\n"
 
     if path.exists() and start_line is not None and end_line is not None:
         """Replaces specified lines in a file with new code."""
-        text = path.read_text()
-
+        # Read file in binary mode to preserve original line endings
+        with open(file_path, 'rb') as f:
+            content = f.read()
+            
+        # Detect original line ending
+        line_ending = detect_line_ending(content)
+        
+        # Decode content for line operations
+        text = content.decode('utf-8')
         lines = text.splitlines(keepends=True)
-
-        # Insert the new code at the start line after converting it into a list of lines
+        
+        # Handle indentation for new code lines
         lines[start_line:end_line] = handle_indent(lines, new_code_lines, start_line, end_line)
+        
+        # Join all lines and encode ensuring all line endings match the original
+        result = ''.join(lines)
+        # Normalize to \n first
+        result = result.replace('\r\n', '\n').replace('\r', '\n')
+        # Then convert to detected line ending
+        if line_ending == b'\r\n':
+            result = result.replace('\n', '\r\n')
+        elif line_ending == b'\r':
+            result = result.replace('\n', '\r')
+            
+        content = result.encode('utf-8')
     else:
-        lines = new_code_lines
+        # For new files, use system default line ending
+        content = ''.join(new_code_lines).encode('utf-8')
 
     # Save the modified contents back to the file
-    save_file_contents(file_path, "".join(lines))
+    save_file_contents(file_path, content)
 
 
 class ModifyCode(Step):
diff --git a/patchwork/test_line_endings.py b/patchwork/test_line_endings.py
new file mode 100644
index 000000000..1ae66321a
--- /dev/null
+++ b/patchwork/test_line_endings.py
@@ -0,0 +1,29 @@
+import tempfile
+import os
+
+def test_line_endings():
+    # Create a test file with CRLF line endings
+    content = "line1\r\nline2\r\nline3\r\n"
+    
+    with tempfile.NamedTemporaryFile(delete=False, mode='wb') as f:
+        f.write(content.encode('utf-8'))
+        temp_path = f.name
+
+    # Now try to modify it using our ModifyCode functions
+    from steps.ModifyCode.ModifyCode import replace_code_in_file
+    
+    # Try to replace the second line
+    replace_code_in_file(temp_path, 1, 2, "new line2\r\n")
+    
+    # Read the result
+    with open(temp_path, 'rb') as f:
+        result = f.read().decode('utf-8')
+    
+    print("Original line endings preserved?" + str("\r\n" in result))
+    print("Result content (in hex):")
+    print(''.join(hex(ord(c))[2:].zfill(2) for c in result))
+    
+    os.unlink(temp_path)
+
+if __name__ == "__main__":
+    test_line_endings()
\ No newline at end of file