diff --git a/perceptionmetrics/utils/segmentation_metrics.py b/perceptionmetrics/utils/segmentation_metrics.py
index 3975e5dd..b55ee5b2 100644
--- a/perceptionmetrics/utils/segmentation_metrics.py
+++ b/perceptionmetrics/utils/segmentation_metrics.py
@@ -255,6 +255,18 @@ def get_averaged_metric(
         """
         metric = getattr(self, f"get_{metric_name}")
         if method == "macro":
+            per_class_values = metric(per_class=True)
+            nan_mask = np.isnan(per_class_values)
+            missing_count = int(np.sum(nan_mask))
+            
+            if missing_count > 0:
+                import warnings
+                # Use implicit string concatenation to keep lines short
+                msg = (
+                    f"Warning: {missing_count} class(es) were missing from the confusion matrix. "
+                    f"Their {metric_name.upper()} evaluated to NaN and will be ignored in the macro-average."
+                )
+                warnings.warn(msg, UserWarning)
             return float(np.nanmean(metric(per_class=True)))
         if method == "micro":
             return float(metric(per_class=False))