diff --git a/exon/exon-sdf/src/io.rs b/exon/exon-sdf/src/io.rs
index ac877167..275ae452 100644
--- a/exon/exon-sdf/src/io.rs
+++ b/exon/exon-sdf/src/io.rs
@@ -71,8 +71,8 @@ mod tests {
     #[tokio::test]
     async fn test_read_record() -> crate::Result<()> {
         let molfile_content = r#"
-Methane
-Example
+    Methane
+    Example
 
 2  1  0  0  0  0            999 V2000
     0.0000    0.0000    0.0000 C   0  0  0  0  0  0
@@ -97,7 +97,7 @@ $$$$
 
         let record = reader.read_record().await?.unwrap();
 
-        assert_eq!(record.header(), "Methane\nExample\n");
+        assert_eq!(record.header(), "Methane\nExample");
         assert_eq!(record.data().len(), 3);
         assert_eq!(record.atom_count(), 2);
         assert_eq!(record.bond_count(), 1);
diff --git a/exon/exon-sdf/src/record.rs b/exon/exon-sdf/src/record.rs
index 7730cd10..23c68724 100644
--- a/exon/exon-sdf/src/record.rs
+++ b/exon/exon-sdf/src/record.rs
@@ -100,7 +100,19 @@ pub(crate) fn parse_to_record(content: &str) -> crate::Result<Record> {
     let mut lines = content.lines();
 
     // Parse header (first 3 lines)
-    let header = lines.by_ref().take(3).collect::<Vec<_>>().join("\n");
+    let header = lines
+        .by_ref()
+        .take(3)
+        .filter_map(|l| {
+            let line = l.trim();
+            if line.is_empty() {
+                None
+            } else {
+                Some(line)
+            }
+        })
+        .collect::<Vec<_>>()
+        .join("\n");
 
     // Parse counts line
     let counts_line = lines.next().expect("Missing counts line");