diff --git a/util.go b/util.go
index 5cc953b..11150a0 100644
--- a/util.go
+++ b/util.go
@@ -203,3 +203,34 @@ func parseSizeInBytes(sizeStr string) uint {
 
 	return safeMul(uint(size), multiplier)
 }
+
+// deepSearch scans deep maps, following the key indexes listed in the
+// sequence "path".
+// The last value is expected to be another map, and is returned.
+//
+// In case intermediate keys do not exist, or map to a non-map value,
+// a new map is created and inserted, and the search continues from there:
+// the initial map "m" may be modified!
+func deepSearch(m map[string]interface{}, path []string) map[string]interface{} {
+	for _, k := range path {
+		m2, ok := m[k]
+		if !ok {
+			// intermediate key does not exist
+			// => create it and continue from there
+			m3 := make(map[string]interface{})
+			m[k] = m3
+			m = m3
+			continue
+		}
+		m3, ok := m2.(map[string]interface{})
+		if !ok {
+			// intermediate key is a value
+			// => replace with a new map
+			m3 = make(map[string]interface{})
+			m[k] = m3
+		}
+		// continue search from here
+		m = m3
+	}
+	return m
+}
diff --git a/viper.go b/viper.go
index b36048d..6efc2b3 100644
--- a/viper.go
+++ b/viper.go
@@ -935,7 +935,13 @@ func SetDefault(key string, value interface{}) { v.SetDefault(key, value) }
 func (v *Viper) SetDefault(key string, value interface{}) {
 	// If alias passed in, then set the proper default
 	key = v.realKey(strings.ToLower(key))
-	v.defaults[key] = value
+
+	path := strings.Split(key, v.keyDelim)
+	lastKey := strings.ToLower(path[len(path)-1])
+	deepestMap := deepSearch(v.defaults, path[0:len(path)-1])
+
+	// set innermost value
+	deepestMap[lastKey] = value
 }
 
 // Set sets the value for the key in the override regiser.
@@ -945,7 +951,13 @@ func Set(key string, value interface{}) { v.Set(key, value) }
 func (v *Viper) Set(key string, value interface{}) {
 	// If alias passed in, then set the proper override
 	key = v.realKey(strings.ToLower(key))
-	v.override[key] = value
+
+	path := strings.Split(key, v.keyDelim)
+	lastKey := strings.ToLower(path[len(path)-1])
+	deepestMap := deepSearch(v.override, path[0:len(path)-1])
+
+	// set innermost value
+	deepestMap[lastKey] = value
 }
 
 // ReadInConfig will discover and load the configuration file from disk