Precise characterization of functional loss in small retinal lesions is difficult with conventional techniques. Using the scanning laser ophthalmoscope, the authors evaluated functional changes and fixation behavior in 26 eyes with macular holes and 15 eyes with macular cysts. A dense scotoma was present over all macular holes; 24 had no detectable functional alteration at the margins of the hole, and fixation was above the horizontal meridian in all eyes. Nine eyes with cysts had no detectable functional loss over the cyst. Only two eyes had small areas of dense scotoma within the cyst area, and four had areas of relative scotoma. Fixation was central in all eyes. Characterization of functional changes is helpful in differentiating holes from cysts. Photocoagulation at the margin of the holes may result in further functional damage.