diff --git a/git_machete/cmd.py b/git_machete/cmd.py
index 03f722b..d5e182f 100644
--- a/git_machete/cmd.py
+++ b/git_machete/cmd.py
@@ -89,7 +89,7 @@ class MacheteClient:
 
     def read_definition_file(self, verify_branches: bool = True) -> None:
         with open(self._definition_file_path) as f:
-            lines: List[str] = [line.rstrip() for line in f.readlines() if not line.isspace()]
+            lines: List[str] = [line.rstrip() for line in f.readlines()]
 
         at_depth = {}
         last_depth = -1
@@ -98,6 +98,10 @@ class MacheteClient:
 
         invalid_branches: List[str] = []
         for index, line in enumerate(lines):
+            # Skip whitespace-only lines for processing but preserve original line numbering
+            stripped_line = line.strip()
+            if not stripped_line:
+                continue
             prefix = "".join(itertools.takewhile(str.isspace, line))
             if prefix and not self.__indent:
                 self.__indent = prefix