The activity and selectivity for the isomerization of heptanes over Pd-loaded SAPO molecular sieves with AEL and AFI structure were investigated. By synthesis of the AEL molecular sieves from Al-isopropoxide, the acid site concentration could be controlled by the amount of silicon in the synthesis gel. The resulting concentration of SiAl-OH groups ranged from 0.07 to 0.3 mmol/g, exhibiting the same acid strength, independent from the acid site concentration. Catalysts were impregnated with 0.1-2 wt.% Pd. The activity increased with increasing Pd content up to a Pd to acid site ratio of 0.02-0.03. Above this value, the metal loading did not influence the activity. A further enhancement of the activity was possible by increasing the number of SiAl-OH acid sites. The selectivity to isomerization was constant for the catalysts with an acid site concentration >0.19 mmol/g. The catalysts synthesized from Al-isopropoxide showed a lower activity compared to the catalysts synthesized from aluminum oxide, probably due to diffusional restrictions caused by the formation of polycrystalline agglomerates.