Three-dimensional imaging of fuel tracer planar laser-induced fluorescence in a homogeneous charge compression ignition (HCCI) engine is presented. A high-speed multiple Nd:YAG laser and detection system, in combination with a scanning mirror, are used to collect eight images, with an equidistant separation of 0.5 mm. Three-dimensional isoconcentration surfaces calculated from the data are visualized. Three-dimensional imaging offers new opportunities to study different combustion events, specifically the topology of flame structures. For example, it is possible to distinguish if separate islands in a fluorescence image really are separate or if it is an effect from wrinkling in and out of the laser sheet. The PLIF images were also analyzed by identifying five intensity ranges corresponding to increasing degrees of reaction progress. The gradual fuel consumption and thus combustion was then analyzed by calculating the volumetric fraction of these intensity ranges for different crank angle positions. The occurrence of multiple isolated iguition spots and the observed gradual decrease in fuel concentration indicates that HCCI combustion relies on distributed reactions and not flame propagation.