A high-precision fraction collector for capillary electrophoresis has been developed. The device utilizes detection close to the end of the capillary and a sheath liquid at the exit of the capillary, allowing continuous collection (i.e., uninterrupted applied electrical field) of multiple species. The role of the sheath liquid flow rate and position of detection in the column on the collection precision was assessed. Fiber-optic detection at approximately 1 cm before the exit end of the capillary was found effective for precise timing of the collection. Up to 60 fractions of microliter or smaller volumes could be automatically collected into capillaries used as collection vials. The collection capillaries were placed on a cylinder, and a computer-controlled stepping motor aligned the appropriate capillary with the column exit. The effectiveness of the fraction collector was demonstrated in the collection of all 11 fragments of the HaeIII restriction digest of phi X-174 plasmid DNA. Polymerase chain reaction amplification of the 271 and 281 bp fragments revealed an inversion of the size-dependent migration order.