The use of metagenomics for virus discovery in clinical samples has opened new opportunities for understanding the aetiology of unexplained illness. This study explores the potential of this sequence-independent approach in a public-health setting, by systematic analysis of samples cultured from patients with unexplained illness through a combination of PCR-based assays and viral metagenomics. In total, 1834 cell-culture isolates were collected between 1994 and 2007 through the Enterovirus Surveillance programme in the Netherlands. During the 13 year period, seven samples that exhibited reproducible cytopathogenic effects in cell culture tested negative in standard PCR assays for a range of viruses. In order to fill the diagnostic gap, viral metagenomics was applied to these culture supernatants, resulting in the rapid identification of viruses in all of the samples. The unexplained samples contained BK polyomavirus, herpes simplex virus, Newcastle disease virus and the recently discovered Saffold viruses (SAFV) (which dominated the unexplained samples; n=4). The full genomic sequences of four SAFV genotype 3 (SAFV-3) viruses, which share 88-93% nucleotide identity with known SAFV-3 viruses, are reported. Further screening for SAFV in additional cultured, unidentified clinical isolates from 2008 and 2009 resulted in identification of another SAFV-positive sample. Although the pathogenicity of the identified viruses has not been established, this study demonstrates that viral metagenomics is a powerful tool that can be integrated into public-health monitoring efforts to investigate unidentified viruses in cell cultures from clinical isolates where standard PCR assays fail to detect viruses.