A series of gold (Au) nanostructures, having different morphologies, were fabricated for amperometric selective detection of carbon monoxide (CO), a biologically important signaling molecule. Au layers were electrodeposited from a precursor solution of 7 mM HAuCl4 with a constant deposition charge (0.04 C) at various deposition potentials. The obtained Au nanostructures became rougher and spikier as the deposition potential lowered from 0.45 V to 0.05 V (vs. Ag/AgCl). As prepared Au layers showed different hydrophobicity: The sharper morphology, the greater hydrophobicity. The Au deposit formed at 0.05 V had the sharpest shape and the greatest surface hydrophobicity. The sensitivity of an Au deposit for amperometric CO sensing was enhanced as the Au surface exhibits higher hydrophobicity. In fact, CO selectivity over common electroactive biological interferents (L-ascorbic acid, 4-acetamidophenol, 4-aminobutyric acid and nitrite) was improved eminently once the Au deposit became more hydrophobic. The most hydrophobic Au was also confirmed to sense CO exclusively without responding to nitric oxide, another similar gas signaling molecule, in contrast to a hydrophobic platinum (Pt) counterpart. This study presents a feasible strategy to enhance the sensitivity and selectivity for amperometric CO sensing via the fine control of Au electrode nanostructures.