Even though various kinds of IPv6 transition mechanisms have been developed for the transition to an IPv6 network, these transition mechanisms take no stance on whether applications support IPv6 or not. This paper describes why the transition period between IPv4 and IPv6 applications may not be straightforward and applications should be ported to support both IPv4 and IPv6; such applications are called "IP version-independent applications." Also, this paper examines and empirically evaluates overhead of the IP version-independent applications, since the performance implication is not well known. The overhead might be very dependent on data sizes and network performance, but it was relatively minimized for general Internet traffic with larger data sizes and lower network latency.