Presented paper deals with infrared thermography (IRT) used for the diagnostics of Carpal Tunnel Syndrome (CTS). More studies on medical thermography in the relation with CTS diagnostics were published. Jesensek Papez B. et al. in 2008 and 2009 improved outcome with classification success rates near to or over 80% in dorsal segments of hand. The background of this study is the skin physiological temperature distribution difference on the dorsal hands and pathophysiological temperature distribution on hands with CTS and non-invasiveness and painlessness of IRT. For presented study, the database of 268 thermal images of the dorsal side of 120 healthy (n= 120) and 14 pathological hands (n=14) with clinically diagnosed CTS of 8 patients were examined. Pre-surgical thermograms of the hands with CTS of each subject were taken and stored by using IRT (Thermocamera Fluke Ti55/20, FLUKE, USA). The new methodology of measurement and evaluation process of thermograms (SmartView 2.1, FLUKE, USA) was assessed. We observed the temperature distribution of the whole hand and the partial temperatures of the center point of carpals (D1), the center point of metacarpals (D2) and the finger tips of the third finger from proximal phalanges (D3), the intermediate phalanges (D4) to the distal phalanges (D5) and the Median Nerve Index (MI=(D1-D5)) were calculated [35]. Results obtained from measurements of the five defined points on the dorsal side of hands showed, that the temperature of CTS hands is characterized by a higher temperature in the phalanges unlike the wrist (MI<0, 71,4%), while the temperature is the lowest on distal phalanges (D5) of healthy hands (MI≥0, 85,8%). The results showed that the skin temperatures of median nerve distribution area on dorsal hands were significantly different between CTS and the control group. The sensitivity of IRT in diagnostic process of CTS is 0,714. Results will be confirmed by further screening of statistically significant group of patients.