Composite structures provide opportunities for weight reduction, material tailoring and integrating control surfaces with embedded transducers, which are not possible in conventional metallic structures. As a result there is a substantial increase in the use of composite materials in aerospace and other major industries, which has necessitated the need for structural health monitoring(SHM) of aerospace structures. In the context of SHM of aircraft structures, there are many areas, which are still not explored and need deep investigation. Among these, one of the major areas is the development of efficient damage models for complex composite structures, like stiffened structures, box-type structures, which are the building blocks of an aircraft wing structure. Quantification of the defect due to porosity and especially the methods for identifying the porous regions in a composite structure is another such area, which demands extensive research. In aircraft structures, it is not advisable for the structures, to have high porosity content, since it can initiate common defects in composites such as, delamination, matrix cracks etc.. In fact, there is need for a high frequency analysis to detect defects in such complex structures and also to detect damages, where the change in the stiffness due to the damage is very small. Lamb wave propagation based method is one of the efficient high frequency wave based method for damage detection and are extensively used for detecting small damages, which is essentially needed in aircraft industry. However, in order, to develop an efficient Lamb wave based SHM system, we also need an efficient computational wave propagation model. Developing an efficient computational wave propagation model for complex structures is still a challenging area. One of the major difficulty is its computational expense, when the analysis is performed using conventional FEM. However, for 1D And 2D composite structures, frequency domain spectral finite element method (SFEM), which are very effective in sensing small stiffness changes due to a defect in a structure, is one of the efficient tool for developing computationally efficient and accurate wave based damage models. In this work, we extend the efficiency of SFEM in developing damage models, for detecting damages in built-up composite structures and porous composite structure. Finally, in reality, the nature of variability of the material properties in a composite structure, created a variety of structural problems, in which the uncertainties in different parameters play a major part. Uncertainties can be due to the lack of good knowledge of material properties or due to the change in the load and support condition with the change in environmental variables such as temperature, humidity and pressure. The modeling technique is also one of the major sources of uncertainty, in the analysis of composites. In fact, when the variations are large, we can find in the literatures available that the probabilistic models are advantageous than the deterministic ones. Further, without performing a proper uncertain wave propagation analysis, to characterize the effect of uncertainty in different parameters, it is difficult to maintain the reliability of the results predicted by SFEM based damage models. Hence, in this work, we also study the effect of uncertainty in different structural parameters on the performance of the damage models, based on the models developed in the present work. First, two SFEM based models, one based on the method of assembling 2D spectral elements and the other based on the concept of coupling 2D and 1D spectral elements, are developed to perform high frequency wave propagation analysis of some of the commonly used built-up composite structures. The SFEM model developed using the plate-beam coupling approach is then used to model wave propagation in a multiple stiffened structure and also to model the stiffened structures with different cross sections such as T-section, I-section and hat section. Next, the wave propagation in a porous laminated composite beam is modeled using SFEM, based on the modified rule of mixture approach. Here, the material properties of the composite is obtained from the modified rule of mixture model, which are then used in SFEM to develop a new model for solving wave propagation problems in porous laminated composite beam. The influence of the porosity content on the parameters such as wave number, group speed and also the effect of variation in theses parameters on the time responses are studied first. Next, the effect of the length of the porous region (in the propagation direction) and the frequency of loading, on the time responses, is studied. The change in the time responses with the change in the porosity of the structure is used as a parameter to find the porosity content in a composite beam. The SFEM models developed in this study is then used in the context of wave based damage detection, in the next study. First ,the actual measured response from a structure and the numerically obtained response from a SFEM model for porous laminated composite beam are used for the estimation of porosity, by solving a nonlinear optimization problem. The damage force indicator (DFI) technique is used to locate the porous region in a beam and also to find its length, using the measured wave propagation responses. DFI is derived from the dynamic stiffness matrix of the healthy structure along with the nodal displacements of the damaged structure. Next, a wave propagation based method is developed for modeling damage in stiffened composite structures, using SFEM, to locate and quantify the damage due to a crack and skin-stiffener debonding. The method of wave scattering and DFI technique are used to quantify the damage in the stiffened structure. In the uncertain wave propagation analysis, a study on the uncertainty in material parameters on the wave propagation responses in a healthy metallic beam structure is performed first. Both modulus of elasticity and density are considered uncertain and the analysis is performed using Monte-Carlo simulation (MCS) under the environment of SFEM. The randomness in the material properties are characterized by three different distributions namely normal, Weibul and extreme value distribution and their effect on wave propagation, in beam is investigated. Even a study is performed on the usage of different beam theories and their uncertain responses due to dynamic impulse load. A study is also conducted to analyze the wave propagation response In a composite structure in an uncertain environment using Neumann expansion blended with Monte-Carlo simulation (NE-MCS) under the environment of SFEM. Neumann expansion method accelerates the MCS, which is required for composites as there are many number of uncertain variables. The effect of the parameters like, fiber orientation, lay-up sequence, number of layers and the layer thickness on the uncertain responses due to dynamic impulse load, is thoroughly analyzed. Finally, a probabilistic sensitivity analysis is performed to estimate the sensitivity of uncertain material and fabrication parameters, on the SFEM based damage models for a porous laminated composite beam. MCS is coupled with SFEM, for the uncertain wave propagation analysis and the Kullback-Leibler relative entropy is used as the measure of sensitivity. The sensitivity of different input variables on the wave number, group speed and the values of DFI, are mainly considered in this study. The thesis, written in nine chapters, presents a unified document on wave propagation in healthy and defective composite structure subjected to both deterministic and highly uncertain environment.