ARGONAUTE (AGO) proteins are integral players in all known small RNA-directed regulatory pathways. Eukaryotes produce numerous types of small RNAs, such as microRNAs (miRNA), small interfering RNAs (siRNA), PIWI-interacting RNAs (piRNAs), scanRNAs and 21U-RNAs, and these RNA species associate with different types of AGO family members, such as AGO, PIWI and group 3 proteins. Small RNA-guided AGO proteins regulate gene expression at various levels, including internal genomic DNA sequence elimination (in ciliates), translational repression (animals), and RNA cleavage (all eukaryotes), which in some cases is followed by DNA methylation and chromatin remodeling. The plant model species Arabidopsis contains ten AGO proteins belonging to three phylogenetic clades. This review covers our current knowledge of plant AGO functions during miRNA- and siRNA-mediated regulation of development and stress responses, siRNA-mediated antiviral immune response, and siRNA-mediated regulation of chromatin structure and transposons.