Details on how fluoride interferes in enamel mineralization are still controversial. Therefore, this study aimed at analyzing the organic contents of fluorosis-affected teeth using Fourier Transformation Infrared spectroscopy. To this end, 10 male Wistar rats were divided into two groups: one received 45 ppm fluoride in distilled water for 60 days; the other received distilled water only. Then, the lower incisors were removed and prepared for analysis by two FTIR techniques namely, transmission and micro-ATR. For the first technique, the enamel was powdered, whereas in the second case one fluorotic incisor was cut longitudinally for micro-ATR. Using transmission and powdered samples, FTIR showed a higher C–H content in the fluorotic enamel compared with control enamel ( p < 0.05, n = 4 in the flurotic, and n = 5 in the control group). Results from the micro-ATR-FTIR spectroscopic analysis on one longitudinally cut incisor carried out at six points reveal a higher C–H bond content at the surface of the enamel, with values decreasing toward the dentine–enamel junction, and reaching the lowest values at the subsuperficial enamel. These results agree with the morphological data, which indicate that in the rat incisor the fluorotic lesion is superficial, rather than subsuperficial, as in the case of human enamel. The results also suggest that the increased C–H bond content may extend toward the more basal enamel (intraosseous), indicating that fluorotic enamel may intrinsically contain more protein. Finally, particularly when coupled to ATR, FTIR is a suitable tool to study the rat incisor enamel, which is a largely used model of normal and abnormal amelogenesis. Further studies along this line may definitely answer some questions regarding protein content in fluorotic enamel as well as their origin.