diff --git a/jcvi/formats/bed.py b/jcvi/formats/bed.py
index df791837..c80ee54c 100755
--- a/jcvi/formats/bed.py
+++ b/jcvi/formats/bed.py
@@ -151,7 +151,7 @@ def __init__(self, filename=None, key=None, sorted=True, juncs=False, include=No
             return
 
         for line in must_open(filename):
-            if line[0] == "#" or (juncs and line.startswith("track name")):
+            if line[0] == "#" or (juncs and line.startswith("track name")) or line.strip()=="":
                 continue
             b = BedLine(line)
             if include and b.accn not in include: