Fluorescent proteins have had a great impact on the way in which plant membrane traffic is studied. Here we review the uses to which these molecules have been put in this field of research and discuss the advantages and pitfalls of particular fluorescent protein derivatives in various applications and plant species. We discuss in detail the need for quantitative estimates of expression level and the potential of fluorescent proteins for quantitative assays of biosynthetic membrane traffic. Detailed descriptions and protocols are provided for the use of the newly developed 2A-based ratiometric polyprotein probes of membrane traffic in conjunction with semiautomated image analysis software packages for quantitative analyses. The ratiometric probes and software are available from the authors.