diff --git a/requirements-conda.txt b/requirements-conda.txt
index 9a005f303..f652cd66f 100644
--- a/requirements-conda.txt
+++ b/requirements-conda.txt
@@ -39,4 +39,4 @@ future==0.16.0
 matplotlib=1.5.3
 pysam=0.15.0
 pybedtools=0.7.10
-PyYAML=3.12
+PyYAML=5.1
diff --git a/requirements-minimal.txt b/requirements-minimal.txt
index bebfaf604..3f9caabd8 100644
--- a/requirements-minimal.txt
+++ b/requirements-minimal.txt
@@ -11,4 +11,4 @@ future==0.16.0
 matplotlib=1.5.3
 pysam=0.15.0
 pybedtools=0.7.10
-PyYAML=3.12
+PyYAML=5.1
diff --git a/requirements-py-docs.txt b/requirements-py-docs.txt
index 07358e4bb..eeafc4f68 100644
--- a/requirements-py-docs.txt
+++ b/requirements-py-docs.txt
@@ -2,5 +2,5 @@ Sphinx==1.4.4
 sphinx-argparse==0.1.15
 sphinx_rtd_theme==0.1.9
 matplotlib==1.5.3
-PyYAML==3.11
+PyYAML==5.1
 mock>=2.0.0