This paper presents an experimental study of frequency and time domain identification algorithms and discusses their effectiveness in structural health monitoring of frame structures using acceleration input and response data. Three algorithms were considered: 1) a frequency domain decomposition algorithm (FDD), 2) a time domain Observer Kalman IDentification algorithm (OKID), and 3) a subsequent physical parameter identification algorithm (MLK). Through experimental testing of a four-story steel frame model on a uniaxial shake table, the inherent complications of physical instrumentation and testing are explored. Primarily, this study aims to provide a dependable first-order and second-order identification of said test structure in a fully instrumented state. Once the characteristics (i.e. the stiffness matrix) for a benchmark structure have been determined, structural damage can be detected by a change in the identified structural stiffness matrix. This work also analyzes the stability of the identified structural stiffness matrix with respect to fluctuations of input excitation magnitude and frequency content in an experimental setting.