Heat shock proteins (HSPs), well-known in respond to various kinds of stress situations, have been widely studied in Drosophila. However, a few reports related to silkworm bombyx mori. Genetic and non-genetic factors affecting on the expression of some HSPs in heat-treated silkworm were studied at the present paper. The mRNA levels of HSPs were quantified by real-time quantitative RT-PCR method and compared with their expression in the proteome profiles. The results showed up-regulation of two small heat shock proteins (sHSPs), HSP19.9 and HSP20.4 and down-regulation of HSP70 in the fat body, testis and ovary of heat exposed larvae. Higher variation of the sHSPs than HSP70 was observed in the different conditions such as heat exposures and genetic backgrounds. Significant difference in the HSP19.9 expression between two breeds was observed which implied the importance of this gene in the genetic differences. There was significant difference between responses of severe and mild heat shocks after 4 h heat recovery. The HSPs expression in male was significantly higher than that in female silkworm larva for all transcript measurements (P < 0.001). Comparison of two methods of quantification showed a fair similarity between HSPs expression in the transcriptome and proteome levels. Nistari breed as a naturally thermo-tolerant breed was expressed lower HSPs than a thermo-sensitive breed.