In this work, pollen mother cells (PMCs) isolated in Arabidopsis thaliana by laser-capture microdissection (LCM) were subjected to transcription profiling by microarray (LMM). PMCs covering all meiotic stages, from leptotene to tetrad, were collected in an Atmcc1 characterized by overexpression of a GCN5-like histone acetylase (AtMCC1). A total of 150 genes showed differential expression in Atmcc1 PMCs as compared to the wild type. Histone hyperacetylation affected the transcription of genes belonging to categories such as the meiotic and mitotic cycle, the ubiquitin-proteasome-system, and the chromatin structure. We also discuss the putative role of ASK1 and RAD51C up-regulation in the meiotic defects observed in Atmcc1. PMC-LMM experiments allowed identification of candidate AtMCC1 targets with known and potential function in meiosis, providing data for further investigation on plant meiosis.