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Hypoxia in tumours may confer resistance to conventional therapies and is associated with a poorer prognosis.MicroRNA expression alterations have been described in cancer and certain microRNAs have shown regulation by hypoxia.We performed a time course exposition to hypoxia (1% oxygen for 16h, 32h and 48h) using MCF7 cancer cell cultures.We also investigated the effect of VHL suppression in RCC4 renal cancer cells by comparing to RCC4 cells transfected with VHL.The microRNA fractions were isolated from total RNA and sequenced using the GA Ⅱanalyser.Gene expression profiles were determined using Illumina WG-6v3 arrays and microRNA arrays v.1.and complemented with mRNA-seq approaches.This led to the identification of 376 different microRNAs andmieroRNA variants in MCF7 samples and 283 in RCC4 and RCC4+VHL cells.Relative microRNA expression analysis showed a set of 36 microRNAs disregulated in all 3 hypoxia times compared to normoxia.A second set of 62 microRNAs appeared to be disregulated from 32h of hypoxia onwards, suggesting a more severe reaction to hypoxia.Concerning RCC4 cells, 102 microRNAs showed differential levels of expression compared to RCC4+VHL cell.Over 1000putative new microRNAs were identified using a novel machine learning algorithm and are being validated.MieroRNA target sequences were identified among genes differentially expressed in hypoxia and correlated with microRNA expression.All this information will enhance our understanding of hypoxia mediated regulation of gene expression.