Since neuroblastomas are intratumorally heterogeneous, the analysis of genetic and biologic features of randomly selected tumor specimen spots may lead to erroneous conclusions. Our purpose was therefore to construct an easily assessable and strictly defined strategy to unify the detection of various molecular markers in paraffin-embedded neuroblastoma samples. We selected tumor specimen spots of highest proliferation activity, that is, hotspots, for the analysis of MYCN amplification status and proliferation-associated molecular markers, such as nestin, which role in neuroblastoma specimens was evaluated for the first time. Using a chromogenic in situ hybridization (CISH) technique, we showed that patients with a MYCN copy number higher than six in anti-Ki-67-detected hotspots have significantly worse overall survival prognosis than patients with low MYCN copy numbers (P=0.0006). The chosen cutoff value of six was shown to dichotomize MYCN-amplified neuroblastomas at least as specifically as Southern blot hybridization, in which amplification was defined by a copy number of ≥10. Interestingly, we also detected without difficulty MYCN-amplified neuroblastic cells in bone marrow samples using the CISH technique. The proliferation activity, assessed with an anti-Ki-67-based proliferation index, was significantly higher in MYCN-amplified than in nonamplified hotspots. The proliferation indices of the hotspots had also a significant correlation with the prognosis (International Classification) and histological type, whereas the proliferation accelerator Id2 did not associate with any of the mentioned parameters. The expression of nestin associated inversely with MYCN amplification (P=0.018), which challenges a previously suggested role of nestin in neuroblastomas. In summary, hotspot focusing provides a means of analyzing proliferation-associated markers in neuroblastomas, and together with the CISH detection of the MYCN copy number enables an easy and reliable examination of MYCN status in neuroblastomas.