diff --git a/Marlin/Configuration_adv.h b/Marlin/Configuration_adv.h
index 6d164c4f5c..afdd684415 100644
--- a/Marlin/Configuration_adv.h
+++ b/Marlin/Configuration_adv.h
@@ -63,14 +63,16 @@
 //This is for controlling a fan to cool down the stepper drivers
 //it will turn on when any driver is enabled
 //and turn off after the set amount of seconds from last driver being disabled again
-//#define CONTROLLERFAN_PIN 23 //Pin used for the fan to cool controller, comment out to disable this function
-#define CONTROLLERFAN_SEC 60 //How many seconds, after all motors were disabled, the fan should run
+#define CONTROLLERFAN_PIN -1 //Pin used for the fan to cool controller (-1 to disable)
+#define CONTROLLERFAN_SECS 60 //How many seconds, after all motors were disabled, the fan should run
+#define CONTROLLERFAN_SPEED 255  // == full speed
 
 // When first starting the main fan, run it at full speed for the
 // given number of milliseconds.  This gets the fan spinning reliably
 // before setting a PWM value. (Does not work with software PWM for fan on Sanguinololu)
 //#define FAN_KICKSTART_TIME 100
 
+// Extruder cooling fans
 // Configure fan pin outputs to automatically turn on/off when the associated
 // extruder temperature is above/below EXTRUDER_AUTO_FAN_TEMPERATURE.
 // Multiple extruders can be assigned to the same pin in which case 
@@ -81,6 +83,7 @@
 #define EXTRUDER_AUTO_FAN_TEMPERATURE 50
 #define EXTRUDER_AUTO_FAN_SPEED   255  // == full speed
 
+
 //===========================================================================
 //=============================Mechanical Settings===========================
 //===========================================================================
diff --git a/Marlin/Marlin_main.cpp b/Marlin/Marlin_main.cpp
index 69f464b296..a3eac5d2ce 100644
--- a/Marlin/Marlin_main.cpp
+++ b/Marlin/Marlin_main.cpp
@@ -374,13 +374,9 @@ void setup()
   
   lcd_init();
   
-  #ifdef CONTROLLERFAN_PIN
+  #if CONTROLLERFAN_PIN > 0
     SET_OUTPUT(CONTROLLERFAN_PIN); //Set pin used for driver cooling fan
-  #endif
-  
-  #ifdef EXTRUDERFAN_PIN
-    SET_OUTPUT(EXTRUDERFAN_PIN); //Set pin used for extruder cooling fan
-  #endif
+  #endif 
 }
 
 
@@ -1963,7 +1959,12 @@ void prepare_arc_move(char isclockwise) {
   previous_millis_cmd = millis();
 }
 
-#ifdef CONTROLLERFAN_PIN
+#if CONTROLLERFAN_PIN > 0
+
+#if CONTROLLERFAN_PIN == FAN_PIN 
+   #error "You cannot set CONTROLLERFAN_PIN equal to FAN_PIN"
+#endif
+
 unsigned long lastMotor = 0; //Save the time for when a motor was turned on last
 unsigned long lastMotorCheck = 0;
 
@@ -1985,34 +1986,16 @@ void controllerFan()
       lastMotor = millis(); //... set time to NOW so the fan will turn on
     }
     
-    if ((millis() - lastMotor) >= (CONTROLLERFAN_SEC*1000UL) || lastMotor == 0) //If the last time any driver was enabled, is longer since than CONTROLLERSEC...   
+    if ((millis() - lastMotor) >= (CONTROLLERFAN_SECS*1000UL) || lastMotor == 0) //If the last time any driver was enabled, is longer since than CONTROLLERSEC...   
     {
-      WRITE(CONTROLLERFAN_PIN, LOW); //... turn the fan off
+        digitalWrite(CONTROLLERFAN_PIN, 0); 
+        analogWrite(CONTROLLERFAN_PIN, 0); 
     }
     else
     {
-      WRITE(CONTROLLERFAN_PIN, HIGH); //... turn the fan on
-    }
-  }
-}
-#endif
-
-#ifdef EXTRUDERFAN_PIN
-unsigned long lastExtruderCheck = 0;
-
-void extruderFan()
-{
-  if ((millis() - lastExtruderCheck) >= 2500) //Not a time critical function, so we only check every 2500ms
-  {
-    lastExtruderCheck = millis();
-           
-    if (degHotend(active_extruder) < EXTRUDERFAN_DEC)
-    {
-      WRITE(EXTRUDERFAN_PIN, LOW); //... turn the fan off
-    }
-    else
-    {
-      WRITE(EXTRUDERFAN_PIN, HIGH); //... turn the fan on
+        // allows digital or PWM fan output to be used (see M42 handling)
+        digitalWrite(CONTROLLERFAN_PIN, CONTROLLERFAN_SPEED);
+        analogWrite(CONTROLLERFAN_PIN, CONTROLLERFAN_SPEED); 
     }
   }
 }
@@ -2036,11 +2019,11 @@ void manage_inactivity()
       }
     }
   }
-  #if( KILL_PIN>-1 )
+  #if KILL_PIN > 0
     if( 0 == READ(KILL_PIN) )
       kill();
   #endif
-  #ifdef CONTROLLERFAN_PIN
+  #if CONTROLLERFAN_PIN > 0
     controllerFan(); //Check if fan should be turned on to cool stepper drivers down
   #endif
   #ifdef EXTRUDER_RUNOUT_PREVENT
diff --git a/Marlin/temperature.cpp b/Marlin/temperature.cpp
index 871bb811f2..78f1a6908f 100644
--- a/Marlin/temperature.cpp
+++ b/Marlin/temperature.cpp
@@ -99,8 +99,8 @@ static volatile bool temp_meas_ready = false;
 #ifdef FAN_SOFT_PWM
   static unsigned char soft_pwm_fan;
 #endif
-#if EXTRUDER_0_AUTO_FAN_PIN > -1 || EXTRUDER_1_AUTO_FAN_PIN > -1 || EXTRUDER_2_AUTO_FAN_PIN > -1
-  static uint8_t extruderAutoFanState = 0; // extruder auto fan state stored as bitmap
+#if EXTRUDER_0_AUTO_FAN_PIN > 0 || EXTRUDER_1_AUTO_FAN_PIN > 0 || EXTRUDER_2_AUTO_FAN_PIN > 0
+  static unsigned long extruder_autofan_last_check;
 #endif  
   
 #if EXTRUDERS > 3
@@ -307,6 +307,73 @@ int getHeaterPower(int heater) {
   return soft_pwm[heater];
 }
 
+#if EXTRUDER_0_AUTO_FAN_PIN > 0 || EXTRUDER_1_AUTO_FAN_PIN > 0 || EXTRUDER_2_AUTO_FAN_PIN > 0
+
+void setExtruderAutoFanState(int pin, bool state)
+{
+  unsigned char newFanSpeed = (state != 0) ? EXTRUDER_AUTO_FAN_SPEED : 0;
+  // this idiom allows both digital and PWM fan outputs (see M42 handling).
+  pinMode(pin, OUTPUT);
+  digitalWrite(pin, newFanSpeed);
+  analogWrite(pin, newFanSpeed);
+}
+
+void checkExtruderAutoFans()
+{
+  uint8_t fanState = 0;
+
+  // which fan pins need to be turned on?      
+  #if EXTRUDER_0_AUTO_FAN_PIN > 0
+    #if EXTRUDER_0_AUTO_FAN_PIN == FAN_PIN 
+       #error "You cannot set EXTRUDER_0_AUTO_FAN_PIN equal to FAN_PIN"
+    #endif
+    if (current_temperature[0] > EXTRUDER_AUTO_FAN_TEMPERATURE) 
+      fanState |= 1;
+  #endif
+  #if EXTRUDER_1_AUTO_FAN_PIN > 0
+    #if EXTRUDER_1_AUTO_FAN_PIN == FAN_PIN 
+       #error "You cannot set EXTRUDER_1_AUTO_FAN_PIN equal to FAN_PIN"
+    #endif
+    if (current_temperature[1] > EXTRUDER_AUTO_FAN_TEMPERATURE) 
+    {
+      if (EXTRUDER_1_AUTO_FAN_PIN == EXTRUDER_0_AUTO_FAN_PIN) 
+        fanState |= 1;
+      else
+        fanState |= 2;
+    }
+  #endif
+  #if EXTRUDER_2_AUTO_FAN_PIN > 0
+    #if EXTRUDER_2_AUTO_FAN_PIN == FAN_PIN 
+       #error "You cannot set EXTRUDER_2_AUTO_FAN_PIN equal to FAN_PIN"
+    #endif
+    if (current_temperature[2] > EXTRUDER_AUTO_FAN_TEMPERATURE) 
+    {
+      if (EXTRUDER_2_AUTO_FAN_PIN == EXTRUDER_0_AUTO_FAN_PIN) 
+        fanState |= 1;
+      else if (EXTRUDER_2_AUTO_FAN_PIN == EXTRUDER_1_AUTO_FAN_PIN) 
+        fanState |= 2;
+      else
+        fanState |= 4;
+    }
+  #endif
+  
+  // update extruder auto fan states
+  #if EXTRUDER_0_AUTO_FAN_PIN > 0
+    setExtruderAutoFanState(EXTRUDER_0_AUTO_FAN_PIN, (fanState & 1) != 0);
+  #endif 
+  #if EXTRUDER_1_AUTO_FAN_PIN > 0
+    if (EXTRUDER_1_AUTO_FAN_PIN != EXTRUDER_0_AUTO_FAN_PIN) 
+      setExtruderAutoFanState(EXTRUDER_1_AUTO_FAN_PIN, (fanState & 2) != 0);
+  #endif 
+  #if EXTRUDER_2_AUTO_FAN_PIN > 0
+    if (EXTRUDER_2_AUTO_FAN_PIN != EXTRUDER_0_AUTO_FAN_PIN 
+        && EXTRUDER_2_AUTO_FAN_PIN != EXTRUDER_1_AUTO_FAN_PIN)
+      setExtruderAutoFanState(EXTRUDER_2_AUTO_FAN_PIN, (fanState & 4) != 0);
+  #endif 
+}
+
+#endif // any extruder auto fan pins set
+
 void manage_heater()
 {
   float pid_input;
@@ -399,56 +466,15 @@ void manage_heater()
     #endif
 
   } // End extruder for loop
-  
-  #if EXTRUDER_0_AUTO_FAN_PIN > -1 || EXTRUDER_1_AUTO_FAN_PIN > -1 || EXTRUDER_2_AUTO_FAN_PIN > -1
-    bool newFanState;
-    #if EXTRUDER_0_AUTO_FAN_PIN > -1
-    // check the extruder 0 setting (and any ganged auto fan outputs)
-    newFanState = (current_temperature[0] > EXTRUDER_AUTO_FAN_TEMPERATURE || 
-            (EXTRUDER_0_AUTO_FAN_PIN == EXTRUDER_1_AUTO_FAN_PIN && current_temperature[1] > EXTRUDER_AUTO_FAN_TEMPERATURE) || 
-            (EXTRUDER_0_AUTO_FAN_PIN == EXTRUDER_2_AUTO_FAN_PIN && current_temperature[2] > EXTRUDER_AUTO_FAN_TEMPERATURE));
-    if ((extruderAutoFanState & 1) != newFanState) // store state in first bit
-    {
-        int newFanSpeed = (newFanState ? EXTRUDER_AUTO_FAN_SPEED : 0);
-        if (EXTRUDER_0_AUTO_FAN_PIN == FAN_PIN) 
-            fanSpeed = newFanSpeed;
-        pinMode(EXTRUDER_0_AUTO_FAN_PIN, OUTPUT);
-        digitalWrite(EXTRUDER_0_AUTO_FAN_PIN, newFanSpeed);
-        analogWrite(EXTRUDER_0_AUTO_FAN_PIN, newFanSpeed);
-        extruderAutoFanState = newFanState | (extruderAutoFanState & ~1);
-    }
-    #endif //EXTRUDER_0_AUTO_FAN_PIN > -1
-    #if EXTRUDER_1_AUTO_FAN_PIN > -1 && EXTRUDER_1_AUTO_FAN_PIN != EXTRUDER_0_AUTO_FAN_PIN
-    // check the extruder 1 setting (except when extruder 1 is the same as 0)
-    newFanState = (current_temperature[1] > EXTRUDER_AUTO_FAN_TEMPERATURE ||
-            (EXTRUDER_1_AUTO_FAN_PIN == EXTRUDER_2_AUTO_FAN_PIN && current_temperature[2] > EXTRUDER_AUTO_FAN_TEMPERATURE));
-    if ((extruderAutoFanState & 2) != (newFanState<<1)) // use second bit
-    {
-        int newFanSpeed = (newFanState ? EXTRUDER_AUTO_FAN_SPEED : 0);
-        if (EXTRUDER_1_AUTO_FAN_PIN == FAN_PIN) 
-            fanSpeed = newFanSpeed;
-        pinMode(EXTRUDER_1_AUTO_FAN_PIN, OUTPUT);
-        digitalWrite(EXTRUDER_1_AUTO_FAN_PIN, newFanSpeed);
-        analogWrite(EXTRUDER_1_AUTO_FAN_PIN, newFanSpeed);
-        extruderAutoFanState = (newFanState<<1) | (extruderAutoFanState & ~2);
-    }
-    #endif //EXTRUDER_1_AUTO_FAN_PIN > -1
-    #if EXTRUDER_2_AUTO_FAN_PIN > -1 && EXTRUDER_2_AUTO_FAN_PIN != EXTRUDER_0_AUTO_FAN_PIN && EXTRUDER_2_AUTO_FAN_PIN != EXTRUDER_1_AUTO_FAN_PIN
-    // check the extruder 2 setting (except when extruder 2 is the same as 1 or 0)
-    newFanState = (current_temperature[2] > EXTRUDER_AUTO_FAN_TEMPERATURE);
-    if ((extruderAutoFanState & 4) != (newFanState<<2)) // use third bit
-    {
-        int newFanSpeed = (newFanState ? EXTRUDER_AUTO_FAN_SPEED : 0);
-        if (EXTRUDER_2_AUTO_FAN_PIN == FAN_PIN) 
-            fanSpeed = newFanSpeed;
-        pinMode(EXTRUDER_2_AUTO_FAN_PIN, OUTPUT);
-        digitalWrite(EXTRUDER_2_AUTO_FAN_PIN, newFanSpeed);
-        analogWrite(EXTRUDER_2_AUTO_FAN_PIN, newFanSpeed);
-        extruderAutoFanState = (newFanState<<2) | (extruderAutoFanState & ~4);
-    }
-    #endif //EXTRUDER_2_AUTO_FAN_PIN > -1
-  #endif // any AUTO_FAN_PIN enabled  
 
+  #if EXTRUDER_0_AUTO_FAN_PIN > 0 || EXTRUDER_1_AUTO_FAN_PIN > 0 || EXTRUDER_2_AUTO_FAN_PIN > 0
+  if(millis() - extruder_autofan_last_check > 2500)  // only need to check fan state very infrequently
+  {
+    checkExtruderAutoFans();
+    extruder_autofan_last_check = millis();
+  }  
+  #endif       
+  
   #ifndef PIDTEMPBED
   if(millis() - previous_millis_bed_heater < BED_CHECK_INTERVAL)
     return;