The relevance of the study is associated with the search for minimally invasive molecular signatures of the dentogingival complex tissue condition in children. A pilot study aimed to identify spectral signatures of protein conformational changes in gingival crevicular fluid from children aged 8–14 years with dental caries and gingival inflammation (gingivitis) based on analysis of the IR spectral Amide III band in a pilot cohort. Gingival crevicular fluid samples collected from 20 children aged 8–14 years with different dental status were analyzed. FTIR spectra were acquired using synchrotron-based Fourier transform infrared spectroscopy in a Bruker Vertex 80/v spectrometer in the range of 3800–700 cm^–1 with a focus on the Amide III region. Spectral deconvolution combined with multivariate analysis was used to estimate the contribution of protein secondary-structure elements. In the pilot cohort, dental caries was associated with a directed increase in the total contribution of components related to β-sheet structures. Based on the summed contributions of the main secondary structure elements, the β-sheet contribution exceeded 50% across the four analytical groups, the disordered component ranged approximately from 21 to 31%, and the contributions of β-turns and α-helical components remained below 10–11%. Inflammatory gingival changes showed a tendency toward a decreased contribution of β-turns and a relative increase in disordered conformations. Thus, the Amide III profile may reflect integral physicochemical changes in proteins of gingival crevicular fluid in individuals with caries and gingivitis. The reported features should be regarded as candidate spectral signatures of a hypothesis-generating nature that require further clinical validation.