Queen breeding has always been one of the main pillars of beekeeping, requiring experience and the use of modern, scientific techniques. The use of advanced tools in queen bee rearing, including breeding cells, significantly impacts various aspects related to the quality, as well as the physiological and morphological parameters of the queen. Additionally, it is widely accepted that queen quality is directly related to their weight and size at birth. Therefore, the purpose of this study was to compare queen rearing in three different sizes (small, medium, and large) and examine the effect of temperature stresses on the expression of heat shock protein genes. To achieve this goal, 36 queens were used in a factorial 3×2 experiment, with three queen sizes (large, medium, and small) and two levels of stress (temperatures below 4°C and above 40°C). The experiment followed a completely randomized design with 6 treatments and 6 repetitions. RNA was extracted from frozen samples of the combined thoracic region of 3 queens to assess its quality. The quality and quantity of the extracted RNA were analyzed using agarose gel and nanodrop, respectively. Subsequently, cDNA was synthesized, and the relative gene expression was analyzed using Real-Time PCR. The results showed that larger queens exhibited greater resistance to heat stress (P=0.01). Under cold stress conditions, no significant difference was observed in terms of queen size. In summary, the size of the queen rearing cells affected tolerance to heat stress but had no effect on cold stress.