The manual process of counting microbial colonies on agar plates can be time-consuming as it is generally performed by scientists using a light box and pen method. The results can vary from operator to operator and are then often manually transferred into a computer for analysis, which can generate transcription errors. To overcome these manual counting and keying issues, automated colony counters have been designed which offer faster and more reproducible results that can be automatically transferred into a computer. However, to ensure the validity of their data, scientists need to establish that their automated colony counting method is as accurate as a precise manual count before they implement any new process into their workflow, especially if the process has to be used in a GMP compliant environment. This study compares a manual colony counting method with an automated colony counter and demonstrates how to validate an automated colony counting method to ensure accuracy of counting results.