The spatial pattern of Fusarium-infected kernels and their mycotoxin contamination was studied in four wheat fields in Germany using geo-referenced sampling grids (12–15 × 20–30 m, 28–30 samples per field) at harvest. For each sample, frequency of Fusarium-infected kernels and spectrum of species were assessed microbiologically; mycotoxin contents were determined by HPLC-MS/MS analysis. Spatial variability of pathogens and mycotoxins was analysed using various parameters including Spatial Analysis by Distance IndicEs (sadie®). Microdochium majus, the most frequent head blight pathogen in 1998, was less frequent in 1999 and could not be detected in kernels from two fields in 2004. Fusarium avenaceum, F. graminearum and F. poae were the most frequent Fusarium species, with 7–8 species per field. The frequency of Fusarium-infected kernels was 3–15% and the incidence of species showed considerable within-field variability. Spatial patterns varied among Fusarium species as well as from field to field. Although pathogens and mycotoxin were often distributed randomly in the field, F. avenaceum, F. graminearum, F. poae, F. sporotrichioides, F. tricinctum and the mycotoxin moniliformin had an aggregated pattern in at least one field. Patterns are discussed in relation to spread of Fusarium species depending on inoculum sources, spore type, kind of dispersal, availability of susceptible host tissue and micro-climate. Sampling of wheat fields for representative assessment of mycotoxins is complicated by random patterns of Fusarium-infected kernels, especially where the frequency of infection is small.