The mRNA expression profile in diagnostic, pretreatment samples from 52 primary nodal diffuse large B-cell lymphomas (DLBCL) were investigated using a commercially available oligonucleotide array (the Affymetrix Genechip HU133A) that contains >22.000 probe sets representing 18.400 transcripts. Hierarchical clustering indicated that 3 subtypes could be distinguishes. These included a GCB type (n=20) that showed an expression profile as similar to germinal center B-cells, an ABC type (n=25) that showed a profile as in vitro activated B-lymphocytes, and an intermediate group, type-3 (n=5) that did not fit into either of these categories. Two samples could not be classified due to inconsistency in clustering. Correlation with the genotype and phenotype showed that markers of germinal center B-cells (CD10, Bcl-6, t(14;18)) were prevalent but not exclusive to the GCB type. By contrast, MUM1 (a marker of terminal B-cell differentiation) was only expressed in the ABC type and in type-3. These results are similar to results obtained using a custom-made, spotted array - the Lymphochip (Alizadeh et al. Nature 2000; Wright et al, PNAS 2003). Comparison with the clinical features indicated that patients with GCB types of lesions showed a better initial response to CHOP or CHOP-like regimens than the remaining patients. However there was no significant difference in over-all survival. It is concluded that gene profiling with Affymetrix Genechips can be used to distinguish between GCB and ABC types of DLBCL and that these subtypes are likely to represent different, biological entities. Affymetrix Genechips should constitute a useful platform for prospective investigations, which are needed to elucidate whether gene profiling in DLBCL can be of use in choosing which treatment should be offered to patients.