β-Lactoglobulin and whey protein isolate (WPI) were heated in aqueous solutions at pH 2 and 7 at 80 °C, spread onto freshly cleaved mica surfaces, and visualized under butanol using atomic force microscopy. Fine-stranded aggregates were formed at pH 2, the diameter of strands being ca. 4 nm for β-lactoglobulin and 10 nm for WPI. At pH 7, aggregates were composed of ellipsoidal particles, regardless of the concentration of added NaCl. This observation supports the previously proposed two-step aggregation model at neutral pH (Aymard, P.; Gimel, J. C.; Nicolai, T.; Durand, D. J. Chim. Phys. 1996, 93, 987−997), consisting of the formation of primary globular particles and the subsequent aggregation of those primary particles. The AFM provides the first direct evidence for the anisotropic shape of these primary particles. The heights of primary particles increased from ca. 11 to 27 nm with increasing concentrations of added NaCl from 0 to 0.3 M in the case of WPI. The rate of aggregation was also accelerated with increasing NaCl concentrations, which appeared to induce transitions in gel networks from fine-stranded toward particulate networks. The present study provides structural information essential for understanding the diverse physical properties of heat-induced whey protein gels.