The transcriptome of the CD34+ cells was determined in a group of 10 patients with the 5q− syndrome using a comprehensive array platform, and was compared with the transcriptome of CD34+ cells from 16 healthy control subjects and 14 patients with refractory anaemia and a normal karyotype. The majority of the genes assigned to the commonly deleted region (CDR) of the 5q− syndrome at 5q31–q32 showed a reduction in expression levels in patients with the 5q− syndrome, consistent with the loss of one allele. Candidate genes showing haploinsufficiency in the 5q− syndrome included the tumour suppressor gene SPARC and RPS14, a component of the 40S ribosomal subunit. Two genes mapping to the CDR, RBM22 and CSNK1A1, showed a >50% reduction in gene expression, consistent with the downregulation of the remaining allele. This study identified several significantly deregulated gene pathways in patients with the 5q− syndrome and gene pathway analysis data supports the proposal that SPARC may play a role in the pathogenesis of the 5q− syndrome. This study suggests that several of the genes mapping to the CDR of the 5q− syndrome play a role in the pathogenesis of this disorder.