Purpose: This study evaluated the effect of residual water included within the FT-IR spectra on the calculation of the degree of conversion (DC) of a self-etching adhesive (SEA). Materials and Methods: FT-IR spectra of a SEA (Adper Prompt SE, 3M ESPE) were obtained for different amounts of dentin powder, agitation times, and light-curing times. The measured DC (mDC) obtained from the IR spectra was compared to the apparent DC (aDC) from the adjusted IR spectra using the water subtraction algorithm (WSA), by which the water absorption band was subtracted from the obtained IR spectrum. Results: When the SEA was mixed with 10 mg of dentin powder, the aDC was significantly higher than the mDC immediately after light curing (paired t-test, p 0.001). With the increase in the amount of dentin powder, the mDC immediately after curing and the difference between the mDC and the aDC gradually increased. The amount of dentin powder, light-curing time, square of light-curing time, and time until measurement were the variables that significantly affected the aDC (linear mixed model, p 0.05). However, the agitation time did not affect the aDC or the difference between the mDC and the aDC, except at 20 s. Conclusion: When the DC of SEA itself is measured with FT-IR, the mDC needs to be adjusted with the water subtraction algorithm. Clinically, SEA needs to be applied under conditions of prolonged contact with the dentin substrate and vigorous and prolonged drying. Keywords: Fourier transform infrared spectrophotometer (FT-IR), water subtraction algorithm, self-etching dentin adhesive, degree of conversion, generalized least squares model