As we are moving towards to the Internet of Things (IoT) era, Wireless Sensor Networks (WSN) in smart buildings delineate the heart of such systems¿ architecture. WSN systems are mature enough to support the IoT vision and different architectural designs and communication protocols are developed to realize this vision. In this paper, two different WSN architectural approaches for smart building systems are presented. In the first one, IPv6 over Low power Wireless Personal Area Networks (6LoWPAN) deployment is used, which is designed specifically for constrained embedded devices. In the second one, the system is developed without the usage of IP. To evaluate these two approaches we implemented a scenario of a smart building environment on top of them. We analyze and compare them, both from theoretical and practical point of view. Finally, as a proof of concept we evaluated them experimentaly in our testbed and we reported our conclusions.