diff --git a/waflib/Configure.py b/waflib/Configure.py
index 052706e4..ef0fdc2a 100644
--- a/waflib/Configure.py
+++ b/waflib/Configure.py
@@ -254,7 +254,10 @@ class ConfigurationContext(Context.Context):
 		:param env: a ConfigSet, usually ``conf.env``
 		"""
 		if not env.PREFIX:
-			env.PREFIX = os.path.abspath(os.path.expanduser(Options.options.prefix))
+			if Options.options.prefix or Utils.is_win32:
+				env.PREFIX = os.path.abspath(os.path.expanduser(Options.options.prefix))
+			else:
+				env.PREFIX = ''
 		if not env.BINDIR:
 			env.BINDIR = Utils.subst_vars('${PREFIX}/bin', env)
 		if not env.LIBDIR: