Code from http://forum.arduino.cc/index.php?topic=129013.15

ArduinoDueInternalTemp

//read the temperature of the integrated sensor on the Arduino DUE

float trans = 3.3/4096;
float offset = 0.8;
float factor = 0.00256;
int fixtemp = 27;

void setup() {
  Serial.begin(9600);
}

void loop() {
  float treal = fixtemp + (( trans * temperatur() ) - offset ) / factor;
  Serial.println(treal);
  delay(10);
}

uint32_t temperatur() {
  uint32_t ulValue = 0;
  uint32_t ulChannel;
  
  // Enable the corresponding channel
  adc_enable_channel(ADC, ADC_TEMPERATURE_SENSOR);

  // Enable the temperature sensor
  adc_enable_ts(ADC);

  // Start the ADC
  adc_start(ADC);

  // Wait for end of conversion
  while ((adc_get_status(ADC) & ADC_ISR_DRDY) != ADC_ISR_DRDY);

  // Read the value
  ulValue = adc_get_latest_value(ADC);

  // Disable the corresponding channel
  adc_disable_channel(ADC, ADC_TEMPERATURE_SENSOR);

  return ulValue;
}