This paper deals with low-invasive temperature monitoring inside freeze dryers. During lyophilization, both the temperature of the freeze-dryer shelves and the temperature of the products have to be measured in order to control the process and to guarantee the product quality. In addition, temperature measurements are essential to obtain reliable information during the development of the freeze-drying receipt and to scale-up the process from the laboratory to the industrial scale. Unfortunately, many constrains make such measurements extremely difficult and not many measuring systems are available; in the paper the main problems related to the temperature measurements, along with some available solutions, are discussed. Then, a low invasive measurement system, that has been specifically developed to measure both the required temperatures, is presented and described.