Two methods for the collection of capillary electrophoresis fractions for analysis by matrix-assisted laser desorption/ionization have been investigated; the first using a novel ion-porous joint design for dropwise fraction collection and the second, a process of electrospray deposition. Sensitivity, shot-to-shot reproducibility, effect of matrix preparation and influence of buffer additives encountered in micellar electrokinetic capillary chromatography (MECC) have been examined using a standard peptide, methionine enkephalin. The direct collection of droplets from the capillary outlet was found to give a superior signal intensity, whereas the electrospray method, in its first stage of development, suffered through dilution effects and excessively wide sample distribution. The target compound was successfully collected by electrospray deposition and results indicated that signal intensity and sample homogeneity would be enhanced if the sprayed output could be collected into the sample wells in its entirety. The advantage of using electrospray deposition for the preparation of matrix layers followed by direct droplet collection onto the electrosprayed matrix was clearly demonstrated by improvements in both sensitivity and shot-to-shot variance in signal intensity across the sample well compared with collection onto spotted matrix. In addition, compatibility of the droplet collection method with MECC was illustrated by the recovery of the compound of interest from a buffer containing 30 mM sodium dodecyl sulphate.