Counting cell colonies is a tedious task when performed with the light microscope. Moreover, unless strict double-blind protocols are adhered to, biased counts are difficult to avoid. Presented here is a computer software application that performs accurate, reproducible cell colony counts with a minimum of user generated bias. The application is based upon the Apple IICX computer system with Image software and AppleScan. Colonies are grown on 24-well plates and prepared in such a way as to permit good quality scanning. The scans are then transferred to Image and the individual colonies in each well are counted. Good correlation with counts done by light microscopy is achieved.