Study on temperature dependencies of viscosity (η) and conductivity (σ) of blood lipoproteins [high‐density lipoprotein (HDL), low‐density lipoprotein (LDL), and very low density lipoprotein (VLDL)] and A‐I apolipoprotein (human and rats) has revealed the presence of the anomalous region at temperature 35–38±0.5°C (Tc). Transition width is 2°C. Viscous flow enthalpy, activation energy (ΔH), and transition enthalpy (ΔHtrans.) as well as thermal coefficients Δη/ΔT and Δσ/ΔT on either side of Tc have been calculated. Transition heat is very low in human HDL, VLDL and apoA‐I, and in LDL it is higher by a factor of 4–5. Some mechanisms of the cortisol interaction with HDL and apoA‐I have been studied by infrared (IR) spectroscopy and conductometry. The hormone has been found to strengthen the tangle → α‐helixes and tangle → β‐structures transitions and increase the ordering of lipids. Therewith, ΔHtrans. rises markedly (13 and more times), and at the same time the anomalous region is shifted by 1–2°C in apoA‐I. The anomalous change of viscosity and conductivity in the physiological temperature range for all lipoprotein fractions and apoA‐I seems to be due to the structural phase transition in both proteins and lipids. In view of the heat capacity jump and a low value of ΔHtrans. in human HDL, one may assume the phospholipids of these particles to exhibit the orientation transition of smectic A↔C type, which is assigned to the second type of phase transition. The structural transition into apoA‐I is likely to contain the elements of phase transition of the first and second types. In human and rat VLDL, the smectic → cholesteric phase transition seems to occur. Enthalpy of viscous flow and structural transition in VLDL is higher for rats than for human. The pH shift of the medium to the neutral region (pH 6.1) results in shifting the anomalous region by 1–2°C. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 348–369, 2001