The pathogen Heterobasidion parviporum causes significant losses to forest industries in Europe and North America. The fungus is spread by basidiospores on fresh stumps where it differentiates into a specialized infection hyphae to colonize its host. This differentiation is driven by recognition and its strategic success lies in its ability to do this rapidly and efficiently. To investigate gene expression pattern during the spore germination stages, mRNA of germinated and ungerminated conidiospores of H. parviporum harvested at distinct developmental time points (18, 36, 72 and 120 h) corresponding to periods of isotropic/germ tube emergence, polarized apical, early and late mycelial lateral branching growth stages was hybridized to macroarrays containing 338 cDNAs from H. parviporum. The results of the statistical analysis identified a total of 24, 39, 38 and 30 genes that were differentially upregulated at 18, 36, 72 and 120 h, respectively, relative to time 0. The number of the downregulated genes was 4, 6, 8 and 13 genes respectively. During isotropic, polarized and mycelial growth stages, majority of the differentially expressed genes belonged to functional categories metabolism (21–32%) and protein formation (21–30%). Real-time polymerase chain reaction (real-time-PCR) data essentially confirmed the macroarray analyses. The real-time-PCR result showed that transcript levels of genes involved in glucose metabolism (phosphoglucomutase), amino acid metabolism (arginase, delta-1-pyrroline-5-carboxylate reductase, sulfur metabolism-negative regulator, imidazoleglycerol phosphate dehydratase) and protein synthesis (40S ribosomal protein S15) were significantly increased during polarized growth (36 h) stage but decreased at early and late stages of mycelial growth (72–120 h). An understanding of the various molecular and physiological processes during the development of H. parviporum spores is an important step towards the goal of identifying novel antifungal strategies.