Gold nanorods (AuNRs) used for biomedical applications could be encountered by biomolecules in the bloodstream, of which IgG is the most abundant antibody. With a view to mitigate their side effect on encountered proteins, the effect of Au concentration (5–40 μM) and functionalization (CTAB-positive;PSS-negative; PEG-neutral) of AuNRs was investigated on the stability of a model protein, IgG (1 μM). Electron microscopic images and particle size analyses indicated least aggregation behavior for PEG-AuNRs, which can be correlated to their neutral charge (from zeta potential analyses) or stearic hindrance of PEG chains. Variations in tryptophan domain were probed by UV–visible absorption and fluorescence quenching studies. Synchronous fluorescence study helped to provide information regarding variations in the hydrophobic region of IgG. The denaturation studies also indicated the stability of AuNR–IgG complex formation. These studies showed that positively charged IgG (pI: 7.8 ± 1.0) was mostly affected by negatively charged PSS-AuNRs and least affected by PEG-AuNRs. This was verified by secondary structural investigations performed using CD and FTIR spectroscopy. For cytotoxicity studies on human lymphocytes, CTAB-AuNRs are known to show higher toxicity compared to PSS-AuNRs and PEG-AuNRs (least). Though PSS-functionalized AuNRs were shown to affect cells to a lesser degree based on the negative charge of cell membrane, they could hamper with positively charged biomolecules in the bloodstream before they reach the target, which must also be considered for choosing the right AuNR functionalization. Thus, this work indicates the effect of different AuNR functionalization on protein and cellular toxicity and stresses the necessity to use neutral particles to mitigate their side effect for theranostic applications. © 2016 Elsevier B.V.