Abstract Surface-enhanced Raman scattering (SERS) of CO adsorbed on roughened gold surfaces has been studied using a Raman microscope with high spatial resolution. Sequentially recorded SERS spectra showed variations of Raman lines in their number, intensity, frequency, and halfwidth. Sometimes, in addition to the band for CO adsorbed at top sites, Raman peaks for bridge-bonded CO appear, showing large intensity fluctuations. Obviously, SERS fluctuations represent a more general property of SERS and point to local restructuring of substrates that changes temporarily the character of adsorption sites and/or their contribution to SERS. The single molecule ‘blinking’ effect is also discussed.