As a critical component of any microarray experiment, scanner performance has the potential to contribute variability and bias, the magnitude of which is usually not quantified. Using Standard Reference Material (SRM) 2,242, which is certified for Raman spectral correction, for monitoring the microarray fluorescence at the two most commonly used wavelengths, our team at the National Institute of Standards and Technology (NIST) has developed a method to establish scanner performance, qualifying signal measurement in microarray experiments. SRM 2,242 exhibits the necessary photostability at the excitation wavelengths of 635 nm and 532 nm, which allows scanner signal stability monitoring, although it is not certified for use in this capacity. In the current study, instrument response was tracked day to day, confirming that changes observed in experimental arrays scanned are not due to changes in the scanner response. Signal intensity and signal-to-noise ratio (S/N) were tracked over time on three different scanners, indicating the utility of the SRM for scanner qualification.