The aromatic and sulfur-containing side chains Trp, Tyr, Phe, Cys, and Met contribute to the CD spectra of peptides and proteins in the amide region, interfering with the analysis for secondary structure. We propose a method to correct the CD spectra of peptides undergoing the helix-coil transition for contributions due to absorbing side chains using singular value decomposition. The method uses the common basis vectors obtained from an analysis of the CD spectra of related peptides without the aromatic and sulfur-containing amino acids. The common basis vectors are fitted to a portion of the CD spectrum of the peptide being corrected, in the range that is unaffected by its sidechain contributions. Then the resulting coefficients from the fitting are used along with the common basis vectors to regenerate the entire corrected spectrum. The method is illustrated for the CD spectra of the peptide sequence acetyl-Y-VAXAK-VAXAK-VAXAK-amide, where X is substituted with the 20 naturally occurring amino acids. This peptide model adopts a random-coil conformation in 2 mm sodium phosphate buffer, pH 5.5, and becomes an alpha helix in methanol/buffer solutions. The difference between the original and corrected spectra shows the contribution from the aromatic and sulfur-containing side chains.