Differential scanning microcalorimetry (DSC) and UV–VIS absorption spectroscopy were used to obtain the characteristics of blood serum from newborn rat’ after maternal treatment with cyclophosphamide in comparison with control. The obtained DSC curves reveal a complex endothermic peak due to the unfolding process of various serum proteins. Thermal profiles and absorption spectra of blood serum are sensitive to the age of newborns as well as to effect of maternal administration of cyclophosphamide. The most significant disturbances in serum proteome were observed for 14-day old newborns. The thermodynamic parameters: enthalpy change (∆H), the normalized first moment (M1) of the thermal transition with respect to the temperature axis and the ratio of C p ex at 70 and 60 °C describing denaturation contributions of globulin forms in respect to unliganded albumin with haptoglobin was estimated. Moreover, the second derivative spectroscopy in the UV region was used to resolve the complex protein spectrum. The differences in blood serum detected by DSC and UV–VIS confirm a potential usefulness of these methods for diagnostic and monitoring changes with age as well as the pathological state of blood serum.