diff --git a/bcl2fastq/handlers/bcl2fastq_handlers.py b/bcl2fastq/handlers/bcl2fastq_handlers.py
index 4165441..8f5ab41 100644
--- a/bcl2fastq/handlers/bcl2fastq_handlers.py
+++ b/bcl2fastq/handlers/bcl2fastq_handlers.py
@@ -125,6 +125,9 @@ def create_config_from_request(self, runfolder, request_body):
                 raise ArteriaUsageException("A output folder was specified by the request, but the configuration "
                                             "does not allow arbitrary output folder to be specified.")
 
+        if os.path.abspath(output) == os.path.abspath(runfolder_input):
+            raise ArteriaUsageException("The specified output path is the same as the input path. This is not allowed!")
+
         if "samplesheet" in request_data:
             samplesheet = request_data["samplesheet"]