In this chapter, a technique is outlined for the use of immunohistochemistry (IHC) followed by multiphoton microscopy (MPM) for the analysis of incidence, length, and 3D orientation of the axoneme of the primary cilium. Although the application presented specifically emphasizes localizations in tenocytes and chondrocytes, the technique is applicable to cells in a wide range of connective tissues. The primary advantages of utilizing MPM as opposed to TEM for these kinds of ciliary analyses are the rapidity of the technique for preparation of the samples and the ability to collect data from multiple cells simultaneously. Using MPM, the axoneme, basal body, and associated centriole can be visualized by specific IHC with localizing antibodies. However, the resolution achieved through TEM analyses allows the complex morphology of the primary cilium to be visualized, and this remains the primary advantage of TEM versus MPM. SHG, which occurs only with MPM, allows visualization of collagen fibrils and is particularly advantageous for localizing primary cilia associated with cells in connective tissues. This, and the deep penetration with less photobleaching, are the primary advantages of MPM compared to confocal microscopy. As with any microscopical technique, the protocol needs to be optimized for any given tissue. In particular, additional antigen retrieval techniques to enhance the unmasking of specific epitopes for antibody binding may be required for adaptation of this approach to other dense connective tissues with complex spatial organizations such as intervertebral disc or meniscus.