Method of sampling and laboratory extraction affects interpretation of grain infestation by storage pests

European-Union countries undergo the process of unifying laws. This is also true for protocols designated for monitoring and evaluation of pests and pesticide risks. This study was aimed at exploring whether different methods of sampling and extracting pests would lead to different pest population estimation. We compared two methods of sampling (surface sampling with cup-sampler vs. subsurface sampling with spear-sampler) and two methods of pests’ extraction from samples (automated sieving vs. Tullgren apparatus) taken from a highly pest infested flat grain store. Overall eight species of mites, seven species of beetles and two species of psocids were identified. The pest population density ranged between 0–12 individuals per sample (200 g) in psocids, 0–14 in beetles and 2–25060 in mites. Surface sampling with cup-sampler was significantly more effective than sampling using subsurface spear-sampler. The number of trapped species was influenced neither by sampling nor by extracting method. This study revealed variation in pest population density and spatial distribution when estimated by different sampling methods thereby indicating necessity for common European protocol for sampling and detection of storage pests.