diff --git a/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java b/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java
index 92a6d054..19c7abf1 100644
--- a/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java
+++ b/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.hdrl;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.SQLFragment;
diff --git a/hdrl/src/org/labkey/hdrl/HDRLManager.java b/hdrl/src/org/labkey/hdrl/HDRLManager.java
index 8452407e..a87737e8 100644
--- a/hdrl/src/org/labkey/hdrl/HDRLManager.java
+++ b/hdrl/src/org/labkey/hdrl/HDRLManager.java
@@ -17,7 +17,8 @@
 package org.labkey.hdrl;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.attachments.InputStreamAttachmentFile;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
@@ -45,7 +46,7 @@
 
 public class HDRLManager
 {
-    private static final Logger LOG = Logger.getLogger(HDRLManager.class);
+    private static final Logger LOG = LogManager.getLogger(HDRLManager.class);
     private static final String HDRL_SENSITIVE_DATA_TIME_WINDOW = "hdrlSensitiveDataDeletionTimeWindow";
     private static final String NUM_OF_DAYS_KEY = "HDRLSensitiveDataDeletionWindow";
     private static final int DEFAULT_NUM_OF_DAYS = 30; //default number of days after which data will be deleted
diff --git a/hdrl/src/org/labkey/hdrl/HDRLModule.java b/hdrl/src/org/labkey/hdrl/HDRLModule.java
index 8e4b7ab3..97d08b3a 100644
--- a/hdrl/src/org/labkey/hdrl/HDRLModule.java
+++ b/hdrl/src/org/labkey/hdrl/HDRLModule.java
@@ -16,7 +16,8 @@
 
 package org.labkey.hdrl;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
@@ -37,7 +38,7 @@
 
 public class HDRLModule extends DefaultModule
 {
-    private static final Logger _log = Logger.getLogger(HDRLModule.class);
+    private static final Logger _log = LogManager.getLogger(HDRLModule.class);
     public static final String NAME = "HDRL";
 
     @Override
diff --git a/ms2extensions/src/org/labkey/ms2extensions/PeptideCountPepXmlDataHandler.java b/ms2extensions/src/org/labkey/ms2extensions/PeptideCountPepXmlDataHandler.java
index b63930e2..75f6d32e 100644
--- a/ms2extensions/src/org/labkey/ms2extensions/PeptideCountPepXmlDataHandler.java
+++ b/ms2extensions/src/org/labkey/ms2extensions/PeptideCountPepXmlDataHandler.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.ms2extensions;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.ExperimentDataHandler;
diff --git a/ms2extensions/src/org/labkey/ms2extensions/PeptideCountUpdater.java b/ms2extensions/src/org/labkey/ms2extensions/PeptideCountUpdater.java
index 32bad2ee..6207590d 100644
--- a/ms2extensions/src/org/labkey/ms2extensions/PeptideCountUpdater.java
+++ b/ms2extensions/src/org/labkey/ms2extensions/PeptideCountUpdater.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.ms2extensions;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
@@ -50,7 +51,7 @@ public class PeptideCountUpdater
 {
     private static final Lock LOCK = new ReentrantLock();
 
-    private static final Logger LOG = Logger.getLogger(PeptideCountUpdater.class);
+    private static final Logger LOG = LogManager.getLogger(PeptideCountUpdater.class);
 
     /** @return error message with any problems encountered during the update */
     public String update(Container container, User user)