Gold nanoparticles (AuNPs) and aptamers are compelling building blocks for analytical assays with desired attributes of selectivity and sensitivity and may theoretically form the basis of instrument-free color-changing assays for any target against which a DNA aptamer has been selected. However, assays for proteins based on these components may be subject to significant interferences from the interaction of proteins with nanoparticles. We found that for three representative protein/aptamer systems—thrombin, apolipoprotein E, and platelet-derived growth factor—pH-dependent aggregation occurred, even in the absence of the aptamer, to differing extents. This effect is most pronounced when proteins display net surface charge (i.e., when pH < pI) but can even be observed at pH = pI when the protein retains regions of positive charge. These interactions of AuNPs and cationic regions on proteins may present an important limitation on the development of AuNP-based analytical assays.