Two characteristics of capillary electrophoresis make the technique attractive for the separation of the components of microscale compartments within living organisms: small sample volume requirements and direct compatibility with biofluids. Indeed, capillary electrophoresis has been used for analysis down to a sub-cellular level. There are also potentially many applications of capillary electrophoresis to biological compartments on a super-cellular scale, which are nevertheless so small that they make analysis by conventional separations techniques difficult or impractical. The analytical challenges in small-scale bioanalysis are first to develop a suitable method for collection of sample and its introduction into the separation capillary, and secondly, to achieve the required separation. Examples reviewed here will primarily focus on the analysis of tear fluid or airway surface liquid, cases in which the amount of sample that can be collected range from around 10 microl to around 100 nl.