The targeting ability of three signals previously shown to support the import of passenger proteins into both mitochondria and chloroplasts was investigated with authentic mitochondrial or chloroplastic proteins. An in vitro dual import assay that maintained import specificity showed that the ability of dual signals to support mitochondrial and chloroplastic import depended on the nature of the passenger protein. All dual targeting signals supported import of their native mature protein as a passenger into both mitochondria and chloroplasts. However the glutathione reductase targeting signal only supported mitochondrial import with the mitochondrial protein alternative oxidase, and chloroplast import with the small subunit of ribulose-1,5-bisphosphate carboxylase / oxygenase. The Arabidopsis histidyl-tRNA synthetase targeting signal only supported mitochondrial import with the alternative oxidase as a passenger, but the small subunit of ribulose-1,5-bisphosphate carboxylase / oxygenase was imported into both mitochondria and chloroplasts. The Arabidopsis asparaginyl-tRNA synthetase supported import of alternative oxidase and the small subunit of ribulose-1,5-bisphosphate carboxylase / oxygenase into both mitochondria and chloroplasts. Analysis of the targeting signals of all known dual targeted proteins using targeting predictions indicates that most of them are more strongly predicted to be chloroplast-targeted. Secondary structure predictions indicate the ability of most dual targeted signals to form both α-helical and β-sheet-type structures, a feature of mitochondrial and plastid targeting signals, respectively. Thus, it appears that a major determinant of dual targeting ability is the nature of the mature or passenger protein.