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Regulated gene expression is key to the orchestrated progression of the cell cycle. Many genes are expressed at specific points in the cell cycle, including important cell cycle regulators, plus factors involved in signal transduction, hormonal regulation and metabolic control. We demonstrate that post-embryonic depletion of Arabidopsis thaliana ARGONAUTE1 (AGO1), the main effector of plant microRNAs, impairs cell division in the root meristem. We utilized the highly synchronizable tobacco (Nicotiana tabacum) BY2 cell suspension to analyze mRNA, small RNAs, and mRNA cleavage products of synchronized BY2 cells at S, G2, M and G1 phases of the cell cycle. This revealed that in plants, only a few miRNAs show differential accumulation during the cell cycle, and miRNA-target pairs were only identified for a small proportion of the more than 13,000 differentially expressed genes during the cell cycle. However, this unique set of microRNA-target pairs could be key to attenuate the expression of several transcription factors and disease resistance genes. We also demonstrate that AGO1 binds to a set of 19 nt, tRNA-derived fragments during the cell cycle progression.