Without a pre-amplification of the clinical sample, such as PCR or virus culture, most microarrays are not sensitive enough for pathogen identification in clinical samples since virus titres normally are below their detection limit. For example, a diagnostic human Papilloma virus (HPV)-specific microarray utilizes an HPV-specific PCR-amplification prior to microarray hybridization [6, 7] . Different PCR-based random amplifications have been developed to achieve enough material for a successful identification [3, 4, 8] . However, studies have shown that PCR-based whole genome amplification (WGA) may generate incomplete coverage of genomes [9] . Instead we used multiple displacement amplification (MDA)-based WGA through isothermal amplification by the Phi29 polymerase [9] . The Phi29 polymerase has the highest processivity rate reported, ,70,000 bases every time it binds [10] and an error rate of only 1 in 10 6 -10 7 bases [11] , allowing for good coverage across genomes [9, 12, 13] . The average length produced is .10 kb compared to #3 kb by the Taq polymerase [9] . Phi29-amplification prior to microarray analysis has been used for human genomic DNA analysis [14, 15, 16] and for bacterial DNA analysis [17, 18] . However, the Phi29 polymerase cannot amplify RNA or short DNA fragments (,2000 bp), such as cDNA generated with random hexamers. To overcome this, the method Whole Transcriptome Amplification (WTA) has included a ligation step prior to amplification [2] resulting in cDNA fragments that are ligated into larger transcriptomes that can be efficiently amplified by the Phi29 polymerase.