Abstract: The physical quality and functionality of shell eggs, pasteurized with heat or a combination of heat and ozone, were assessed during eight weeks of storage at 4 or 25 °C. Shell eggs were treated as follows: (1) immersion heating that mimics commercial pasteurization processes (egg internal temperature of 56 ± 0.1 °C for 32 min), or (2) a newly developed combination process comprised of heating (56 ± 0.1°C, internal, for 10 min) followed by gaseous ozone treatment. Eggs were tested for yolk index, Haugh units, albumen pH, albumen turbidity, and percent overrun. Additionally, albumen samples were assayed for lysozyme activity and free sulfhydryl group content, and were analyzed using differential scanning calorimetry and Fourier transform infrared (FTIR) spectroscopy. Both processed and unprocessed eggs maintained superior quality when stored at 4 °C, as opposed to 25 °C. Pasteurization, regardless of method, led to superior maintenance of Haugh units during storage but also increased albumen opacity and decreased albumen overrun. Detrimental effects on quality markers were more severe in heat-pasteurized eggs than those treated with the ozone-based process. Pasteurization of shell eggs by either process did not affect lysozyme activity or sulfhydryl group content. Changes in protein secondary structure, as indicated by FTIR analysis, suggest that the ozone-based process is less damaging to albumen proteins than is the heat-alone process. In conclusion, heat-ozone pasteurization, by virtue of its less severe heat treatment, yields a safe final product that more closely resembles untreated shell eggs.