The heat shock protein families (HSPs) are known regulatory protein, which were related with protein folding, transport and aggregation in the cells after heat, mechanical or metabolic stress and exercise. HSP responses to exercise in men who have different levels of physical activity are not clearly defined. The aim of this study was to compare blood HSPs mRNA levels following one bout of high intensity interval training (HIIT) in physically active (PA) and inactive (I) men. Healthy young men (aged between 22 and 38 years) who defined the exercise duration more than 4 hours per week at least one year was accepted as PA group (n=9) and lower than 1.5 hours per week was accepted as I group (n=9). Peak oxygen consumption (VO2 peak) was measured at the first day, HIIT comprising 4 repeats of a Wingate test (0.050 kg load/kg) was performed at the second day by a cycle ergometer. mRNA levels of HSP27, HSP60, HSP70, HSP90, TNFα, IL6, P53, BCL2, BAX, Caspase 3, Caspase 8 were determined by quantitative real-time PCR analysis, and lactate levels were measured by enzymatic method in blood samples taken before HIIT, 5th min and 24 h after the HIIT. Values are means ± SD. The relative fold changes compared by using one-way ANOVA, Duncan test, differences with in groups were analysed independent samples t test and analysis of covariance. VO2 peak was higher in PA group than I group (37.0±6.0 ml/min/kg vs. 25.5±4.1 ml/min/kg; p=0.023, respectively). Lactate levels at 5 min in both groups were significantly higher than baseline and 24 h lactate levels (p<0.001 for all comparisons). Relative fold changes of HSP27 were elevated in PA and I groups at 5th min and 24 h of post-exercise (PPA= 0.020, PI= 0.001). HSP60 values were higher than baseline at 5th min and 24 h after the HIIT in I group (PI= 0.0001). HSP70 was higher at 5th min in comparison to the baseline in PA group (PPA= 0.024). When compare two groups, relative fold change of HSP70 was higher in PA group than I group (P=0.026) and HSP60 was higher in I group than PA group (P=0.017) at 5th min after the HIIT. HSP90 were similar to baseline after post-exercise in both groups. At 5th min, elevated P53, BCL2, BAX, Caspase 3, Caspase 8 have been shown both in PA and I groups and elevated TNFα and IL6 were found only in the I group (p<0.05 for all comparisons). The findings of this study indicate that physical activity status may alter HSP response in men. HSP60 that is known as mitochondrial HSP, may be more effective on apoptotic and inflammatory changes following HIIT in inactive men but HSP70 may be effective on apoptotic function in physically active men.