Reliable autofocus is required to obtain accurate measurements of fluorescent stained cellular components from a system capable of scanning multiple microscope fields. Autofocus could be performed directly with fluorescence images, but due to photobleaching and destructive fluorescence by-products, it is best to minimize fluorescence exposure for photosensitive specimens and live cells. This exposure problem could be completely avoided by using phase-contrast microscopy, implemented through the same optics as fluorescence microscopy. The purpose of this work was to evaluate functions for both phase-contrast and fluorescence autofocus and determine the suitability of phase-contrast autofocus for fluorescence microscopy. Eleven autofocus functions were independently evaluated for fluorescence and phase-contrast microscopy. The most suitable functions were then chosen from these and phase-contrast and fluorescence autofocus were compared on scans each comprising more than 1,000 microscope fields. Autofocus standard deviation (S.D.) of better than 100 nm was achieved for both phase contrast and fluorescence. There was a measurable difference between the best focus positions in the two modes, but the difference was constant enough to be measured and corrected, suggesting the possibility of using phase contrast to predict best focus in fluorescence microscopy. The scanning experiments also showed that autofocus can be performed at least as fast as 0.25 s/field without loss of precision. © 1994 Wiley-Liss, Inc.