Recently the multi-planet system OGLE-06-109L has been discovered,where the two planets show similarities with theJupiter-Saturn configuration of our Solar System. The orbital parameters of this new system indicate a high inclination for the outer planet. In this parameter study we show the stability of the two planets fordifferent relative inclinations and semi-major axes of the twoplanets. Using the errors in semi-major axes given by the observations, the best result concerning dynamical stability has been obtained when planet b is at 2.1 AU and planet c at 5.1 AU. The worstresult has been found for the closest configuration, when planet b is at 2.5 AU and planet c at 4.1 AU. The second part of this study examines the stability of test planets in the so-called habitable zone (HZ). This is the region around a star where liquid water is stable on the surface of an Earth-like planet.The stability of test-planets in the HZ is shown for different relative inclinations (up to 50°) of the two giant planets inOGLE-06-109L system and then compared to the results of a similar study in the Jupiter-Saturn system. For high relative inclinationswe observe strong perturbations in the HZ in both results, which is probablycaused by the Kozai resonance.In the OGLE-06-109L system we also observe secular perturbations for low inclinations around 0.3 AU. Forcertain mutual inclinations of the two giant planets we have found nearlycircular planetary motion in the HZ.