The first dehydration of protonated glycerol taking place at its secondary site was investigated by density functional calculations by considering different conformations of glycerol. Five parallel reaction pathways via different conformers of protonated glycerol were found. One of these pathways leads to a direct formation of protonated 3-hydroxylpropanal (HPA), another one of these pathways produces protonated glycidol, and the other three produce protonated 3-hydroxy-1,1-propanediol (HPD). One of these pathways producing protonated HPD was found to have obviously larger relative reaction rate than other pathways. The dehydration of protonated HPD to afford protonate HPA requires a rather low reaction barrier (12 kcal/mol). These results show that the production of HPA via a stepwise process with protonated HPD as a key intermediate, is energetically favorable than via a one-step concerted process producing HPA.