Low uniformity in illumination across the image plane impairs the ability of a traditional epifluorescence microscope to quantify fluorescence intensities. Two microlens arrays (MLAs) were introduced into the illumination path of two different epifluorescence microscope systems to improve the uniformity of the illumination. Measurements of the uniformity of illumination were performed with a CCD camera in the focal plane and with fluorescent beads in the image plane. In semi critical alignment, a uniformity of illumination of 15-23% was found compared with 1-2% in the modified system. Coefficient of variation (CV) of fluorescent beads measured on the unmodified system was 20.4% AE 5.3% in semi critical alignment and 10.8% AE 1.3% in Koehler alignment. On the MLA systems, CV was 7.9% AE 2.0% and on a flow cytometer, the CV was 6.7% AE 0.7%. Implementation of MLAs in an epifluorescence microscope improves the uniformity of illumination, thereby reducing the variation in detection of fluorescent signals of the measured objects and becomes equivalent to that of flow cytometry. ' 2012 International Society for Advancement of Cytometry Key terms microlens array; coefficient of variation; epifluorescence microscopy; homogeneous illumination profile; beam shaping; flat top IN a traditional epifluorescence microscope, there is a tradeoff between the illumination uniformity and power. Koehler illumination is used to achieve high uniformity at the expense of illumination intensity, whereas semi-critical alignment is used to achieve high illumination intensity at the expense of uniformity (1). In Koehler illumination, the light source is focused onto the back pupil of the objective, while in semi-critical illumination, the light source is focused slightly beyond the sample. Poor uniformity results in large spatial intensity variations at the focal plane, while low illumination intensity requires longer illumination times and results in additional bleaching of the sample. With Koehler alignment, an improvement in CV can be obtained (2). If a better CV is needed, the signal can be corrected by shading correction (3,4) or by using the middle 50% of the image (5) to reduce the CV down to 3%. Multiplication is effective in cases where the illumination profile is well known and the signals are bright. In cases where the signal is dim, multiplication is not effective because signal to noise ratio is not changed. Reduction of the field of view increases the time needed for acquisition. A hardware solution that improves the CV without any of these disadvantages is desired. Previously, a double microlens array (MLA) was used to improve the uniformity of the illumination from a tungstenhalogen lamp (6) and from lasers (7). Here, we demonstrate that epifluorescence microscopes equipped with a mercury arc lamp can be retrofitted with a double MLA system to achieve the uniformity of Koehler alignment, while achieving the illumination intensity of semi-critical alignment. The need for such improvements arises from our desire to i...