The fractal dimension of a particle aggregate can provide fundomental information on the structure and origin of the aggregate. The analysis of large chemically homogeneous fractal objects has been achieved, but reliable methods of estimating the fractal dimensions of large and chemically heterogeneous aggregates are needed. To this end, we used confocal scanning laser microscopy in which thin optical sections of aggregates were obtained in order to calculate their 2D and ultimately 3D fractal dimensions according to the Mandelbrot theory. Fractal dimensions of 2.08 ± 0.11 for a Brownian aggregation of latex particles and 2.25 ± 0.12 for shear aggregation were determined using the confocal technique. These values are within the ranges for universality classes predicted for such aggregates and observed by previous investigators. Thus, this method appears to provide reliable estimates of the fractal dimension with particular utility in the characterization of aggregates composed of larger particles or complex materials where the fractal dimension may not be accessible by light-scattering measurements. The confocal method is used to analyze flocs of activated sludge material as one example of the application of this method to more complex, large (up to 500 μm), and chemically heterogeneous flocs.