While temporal lobe epilepsy (TLE) has been treatable with anti-seizure medications over the past century, there still remain a large percentage of patients whose seizures remain untreatable pharmacologically. To better understand and treat TLE, our laboratory uses several in vivo analytical techniques to estimate connectivity in epilepsy. This paper reviews two different connectivity-based approaches with an emphasis on application to the study of epilepsy. First, we present effective connectivity techniques, such as Granger causality, that has been used to assess the dynamic directional relationships among brain regions. These measures are used to better understand how seizure activity initiates, propagates, and terminates. Second, structural techniques, such as magnetic resonance imaging, can be used to assess changes in the underlying neural structures that result in seizure. This paper also includes in vivo epilepsy-centered examples of both effective and anatomical connectivity analysis. These analyses are performed on data collected in vivo from a spontaneously seizing animal model of TLE. Future work in vivo on epilepsy will no doubt benefit from a fusion of these different techniques. We conclude by discussing the interesting possibilities, implications, and challenges that a unified analysis would present.