In the present study, we analyzed the effects of 22 microsatellite DNA loci on behavior responses and plasma concentration of hormones related to stress and metabolism following transport trial in pigs. These subjects were selected from the segregating F2 generation of a Pietrain (PIE) x Erhualian (EHL) cross, and the two swine strains differ in stress tolerance. A so-called Backtest Score (BS) at 3, 10 and 17 days after birth (BS3, BS10 and BS17) was implemented to assess the behavior responses for each piglet. Plasma concentrations of Insulin, ACTH, Cortisol, T3 and T4 in pigs were measured after the 2 hours' transport. One-way ANOVA was applied to analyze the relation between microsatellite polymorphisms and stress tolerance markers including BS and concentration of hormones. The results revealed that the allelic number was 3-8, heterozygosity was 0.4155-0.7432 and polymorphism information content was 0.3651-0.8150. SW1808 (P<0.01) and SW0320 (P<0.05) had significant effect on ACTH. The effect of SW1303 on Insulin, SW1092 on Cortisol, SW0320 on T3, S0101 on T4, and SW2446 on BS3 reached a significant level at P<0.05, respectively. The effects of SW2446 (P<0.01), SW1816 (P<0.05) and SW0092 (P<0.05) on BS10 were significant, and the effects of SW2108, SW1816 and SW1023 on BS17 were also significant (P<0.05). Our study suggested that these 11 microsatellites in swine were closely associated with behavior responses and stress tolerance in response to transport.