Micro-thermal analysis (μTATM) is a technique in which thermal analysis is performed on surfaces of test specimens on a small (ca. 2×2 μm) scale. Like any thermal analysis technique, interpretation of results benefits from accurate temperature information and knowledge of the precision of the resultant measurement. However, temperature calibration for such methods is more challenging than with its macro relatives since the calibrant comes into direct contact with the AFM sensor. This paper describes suitable calibration procedures for different types of transitions namely for first order transitions (melting points) and for glass transition temperatures using organic chemicals and polymers.