diff --git a/root_pandas/readwrite.py b/root_pandas/readwrite.py
index ddc6dc0..cb163ec 100644
--- a/root_pandas/readwrite.py
+++ b/root_pandas/readwrite.py
@@ -81,6 +81,9 @@ def expand_braces(orig):
 
 
 def get_nonscalar_columns(array):
+    if len(array) == 0:
+        return []
+
     first_row = array[0]
     bad_cols = np.array([x.ndim != 0 for x in first_row])
     col_names = np.array(array.dtype.names)
@@ -246,6 +249,8 @@ def genchunks():
             current_index = 0
             for chunk in range(int(ceil(float(n_entries) / chunksize))):
                 arr = root2array(paths, key, all_vars, start=chunk * chunksize, stop=(chunk+1) * chunksize, selection=where, *args, **kwargs)
+                if len(arr) == 0:
+                    continue
                 if flatten:
                     arr = do_flatten(arr, flatten)
                 yield convert_to_dataframe(arr, start_index=current_index)
diff --git a/tests/test_issues.py b/tests/test_issues.py
new file mode 100644
index 0000000..2e52f59
--- /dev/null
+++ b/tests/test_issues.py
@@ -0,0 +1,16 @@
+import os
+
+import pandas as pd
+import root_pandas
+
+
+def test_issue_63():
+    df = pd.DataFrame({'a': [], 'b': []})
+    root_pandas.to_root(df, 'tmp_1.root', 'my_tree')
+    df = pd.DataFrame({'a': list(range(10)), 'b': list(range(10))})
+    root_pandas.to_root(df, 'tmp_2.root', 'my_tree')
+    result = list(root_pandas.read_root(['tmp_1.root', 'tmp_2.root'], 'my_tree', where='a > 2', chunksize=1))
+    assert len(result) == 7
+    assert all(len(df) == 1 for df in result)
+    os.remove('tmp_1.root')
+    os.remove('tmp_2.root')