Mycelia of filamentous fungi explore new substrates by means of growing hyphae. These hyphae secrete enzymes that degrade organic material into small molecules that can be taken up to serve as nutrients. Previously, it has been shown that only part of the exploring hyphae of Aspergillus niger highly express the glucoamylase gene glaA. This was a surprising finding considering the fact that all hyphae were exposed to the same environmental conditions. Using reporter studies, we have demonstrated that the expression of other secretion enzyme encoding genes in A. niger is also heterogenic. Co-expression studies showed that hyphae that highly express one of these genes also highly express other genes encoding secreted proteins. Over and above this, high expression of genes encoding secreted proteins correlated with high expression of a gene involved in central metabolism and with high ribosomal RNA content. This suggests that there are populations of hyphae at the periphery that differ in their transcriptional and translational activities. These studies were extended with whole genome transcription profiling of individual hyphae. In order to perform (sub)-cellular transcriptomics on single exploring hyphae, protocols have been set up to collect individual hyphae using LPC, isolate RNA and amplify cDNA. Microarray analysis led to the conclusion that exploring neighboring hyphae are highly heterogenic in gene expression. Genes with heterogenic expression can be found in all functional gene classes.