The mammalian CLC family of chloride transport proteins has been shown to include members with proton transport activity by us and others. To simplify characterization of its properties, we set up a BCECF-based assay to measure proton transport activity in Xenopus oocytes. Our system used a photodiode detector to monitor emission at 512-560 nm, while BCECF was excited with 475 nm. This did not allow ratiometric measurements, but was considerably faster than a setup consisting of a TILL monochromator and video imaging. It also allowed online monitoring of transport activity at high resolution and with low noise using a simple A/D interface. Although albino oocytes gave much stronger fluorescence signals, measurements were also possible with regular, pigmented oocytes. The methods used so far made solution exchange difficult. Our setup even allowed fast solution exchange to bicarbonate-buffered solutions. This setup will simplify the characterization of mutants of proteins transporting acid/base equivalents.