diff --git a/README.md b/README.md
index cf0654d..43f34c7 100644
--- a/README.md
+++ b/README.md
@@ -35,6 +35,16 @@ Development Installation
 
     ./gradlew tasks
 
+Configuring Logging
+===================
+
+Logging is provided using the logback library. The `logback.xml` file in `src/dist/lib/config/` provides a default configuration for the command line tool.
+In release and snapshot artifacts, `logback.xml` is in `lib/config/`.
+You can configure logging by editing the provided `logback.xml` or by specifying the path to a different file::
+
+JAVA_OPTS="-Dlogback.configurationFile=/path/to/external/logback.xml" \
+    bioformats2raw ...
+
 Eclipse Configuration
 =====================
 
@@ -42,6 +52,8 @@ Eclipse Configuration
 
     ./gradlew eclipse
 
+2. Add the logback configuration in `src/dist/lib/config/` to your CLASSPATH.
+
 Usage
 =====
 
diff --git a/build.gradle b/build.gradle
index 9328419..07693e3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -74,6 +74,18 @@ distributions {
     }
 }
 
+startScripts {
+  // placing logback.xml somewhere under src/dist/lib/ keeps it out of
+  // raw2ometiff-*.jar but automatically includes it in the distribution zip
+  // the directory containing logback.xml must be explicitly added to the
+  // startup scripts' classpath, otherwise it will not be detected
+
+  // a subdirectory of 'src/dist/lib/' (not just 'src/dist/') is necessary,
+  // likely due to https://issues.gradle.org/browse/GRADLE-2991
+  // see also discussion in https://github.com/glencoesoftware/bioformats2raw/pull/169
+  classpath += files('src/dist/lib/config/')
+}
+
 publishing {
     publications {
         raw2ometiff(MavenPublication) {
diff --git a/src/main/resources/logback.xml b/src/dist/lib/config/logback.xml
similarity index 100%
rename from src/main/resources/logback.xml
rename to src/dist/lib/config/logback.xml