diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2bc39a0c6..e59f4ede0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,10 @@
     appear in the final output CSV. Keep columns that are not id, weight,
     covariate, or outcome columns will be placed into ``ignore_columns`` during
     processing but are still retained and available in the output.
+- **Clarified `_prepare_input_model_matrix` argument docs**
+  - Updated docstrings in `balance.utils.model_matrix` with
+    explicit descriptions for `sample`, `target`, `variables`, and `add_na`
+    behavior when preparing model-matrix inputs.
 
 ## Bug Fixes
 
@@ -57,6 +61,11 @@
     like `a`, `a_1`, and repeated `a` names appear together.
   - Duplicate columns are now renamed deterministically to guaranteed-unique
     names, preventing downstream clashes after formula sanitization.
+- **`model_matrix` empty-sample errors now raise `ValueError`**
+  - `_prepare_input_model_matrix()` now raises a deterministic `ValueError`
+    when the input sample has zero rows, instead of relying on an assertion.
+  - This aligns runtime behavior with documented exceptions and avoids
+    optimization-dependent assert behavior.
 
 ## Tests
 
diff --git a/balance/utils/model_matrix.py b/balance/utils/model_matrix.py
index 74e72bee6..d4a32dc5a 100644
--- a/balance/utils/model_matrix.py
+++ b/balance/utils/model_matrix.py
@@ -285,14 +285,34 @@ def _prepare_input_model_matrix(
         - Add na indicator if required.
 
     Args:
-        sample (pd.DataFrame | Any): This can either be a DataFrame or a Sample object. TODO: add text.
-        target (pd.DataFrame | Any | None, optional): This can either be a DataFrame or a Sample object.. Defaults to None.
-        variables (List[str] | None, optional): Defaults to None. TODO: add text.
-        add_na (bool, optional): Defaults to True. TODO: add text.
-        fix_columns_names (bool, optional): Defaults to True. If to fix the column names of the DataFrame by changing special characters to '_'.
+        sample (pd.DataFrame | Any): Input sample data as either a
+            ``pandas.DataFrame`` or a ``Sample`` object from
+            ``balance.sample_class`` (recognized via ``_isinstance_sample``).
+        target (pd.DataFrame | Any | None, optional): Optional target data as
+            either a ``DataFrame`` or a ``Sample`` object. If provided, the
+            model-matrix inputs are prepared from a sample/target union of
+            variables and rows. Defaults to None.
+        variables (List[str] | None, optional): Variables to use from both
+            inputs. If provided, `choose_variables` validates that each
+            requested variable exists in both sample and target (when target is
+            supplied), otherwise it raises ``ValueError``. For ``Sample``
+            inputs, this validation/inference is based on covariate names
+            (``sample.covars().names()``), not all raw ``._df`` columns. If
+            None, variables are inferred by `choose_variables`.
+        add_na (bool, optional): If True, add NA indicator columns before
+            model-matrix creation. If False, drop rows containing missing
+            values; this can raise ``ValueError`` if dropping rows empties the
+            sample or target. Defaults to True.
+        fix_columns_names (bool, optional): Whether to sanitize column names by
+            replacing non-word characters with ``_`` and making duplicate names
+            unique. Defaults to True.
 
     Raises:
-        Exception: "Variable names cannot contain characters '[' or ']'"
+        ValueError: If requested ``variables`` are not present in the
+            provided input frame(s) (and in both sample and target when target
+            is supplied), if variables contain ``[`` or ``]``, or if
+            ``add_na=False`` drops all rows from sample/target, or if
+            sample has zero rows.
 
     Returns:
         Dict[str, Any]: returns a dictionary containing two keys: 'all_data' and 'sample_n'.
@@ -312,7 +332,8 @@ def _prepare_input_model_matrix(
         sample_df = sample._df
     else:
         sample_df = sample
-    assert sample_df.shape[0] > 0, "sample must have more than zero rows"
+    if sample_df.shape[0] == 0:
+        raise ValueError("sample must have more than zero rows")
     # NOTE: .copy() not needed as it is copied anyway in _concat_frames
     sample_n = sample_df.shape[0]
     sample_df = sample_df.loc[:, variables]
diff --git a/tests/test_util_model_matrix.py b/tests/test_util_model_matrix.py
index 05b7a05f4..03b859f09 100644
--- a/tests/test_util_model_matrix.py
+++ b/tests/test_util_model_matrix.py
@@ -290,9 +290,9 @@ def test_model_matrix(self) -> None:
             t,
         )
 
-        # Test zero rows warning:
+        # Test zero rows error:
         self.assertRaisesRegex(
-            AssertionError,
+            ValueError,
             "sample must have more than zero rows",
             model_matrix,
             pd.DataFrame(),