* Since the technique involves the use of SDS-PAGE which utilizes the effect that sodium-dodecyl sulfate has on proteins which is to denature them, there is the possibility of dissociating protein factors that possess multiple subunits through the process. This could end up affecting how well the protein factor binds to DNA in later steps of the technique. 
* Not all proteins renature during the transfer process to the nitrocellulose membranes after separation via SDS-PAGE. This area of protein renaturation is still being experimented with.
* Also being experimented with is reusability of southwestern blots to test proteins with a variety of DNA probes before disposal. However, the main challenge is putting together a scheme that outlines conditions that can remove previously used probes from the blot without the expense of denaturing the proteins or extracting them.