Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) were used to monitor changes in the secondary structure and thermal stability of β-lactoglobulin A and B in the presence of sodium dodecyl sulphate (SDS), N-ethylmaleimide (NEM), urea and cysteine. An increase in the thermal stabilities of both proteins was noted in the presence of 10 mM-SDS. In the presence of 50 mM-SDS, there was extensive denaturation of both variants. In general, the β-strand/β-sheet regions in the secondary structure of both variants were very susceptible to denaturation by SDS and cysteine, suggesting that these regions may be held by hydrophobic and disulphide bonds. At ambient temperature and physiological pH, a notable difference was observed in the 1636 and 1627 cm−1 regions of the FTIR spectra of the two β-lg variants. The results suggest possible differences in the nature of the β-sheet/β-strand distribution/content of the two proteins. Urea and NEM at a concentration of 50 mM, had little effect on the secondary structure and denaturation of both variants. New findings are presented which further indicate that although the β-lg B variant showed greater thermal stability than the A variant in all the cases studied, its denaturation temperature and secondary structure were affected to a greater extent by the protein perturbants than β-lg A.