Due to the lack of an effective cure for human immunodeficiency virus (HIV-1), with approximately twenty million new infections expected by 2031, research has moved towards optimised prevention strategies. Drug transporters, characterised extensively in the human liver, kidney and gastrointestinal tract, can be manipulated to improve the pharmacokinetic properties of orally delivered anti-retrovirals (ARV's). There is paucity in knowledge of drug transporter expression in the human cervicovaginal (CV) tract and representative pre-clinical models, where characterisation and manipulation may enable optimisation of topically applied ARVs for prevention of sexual transmission of HIV-1. In this thesis, RT-qPCR was used to characterise drug transporter profiles of CV pre-clinical models (in vitro, ex vivo and in vivo) for comparison with human CV tissue profiles, where distinguishable differences were observed, most notably in the efflux transporters P-gp and MRP2-4. This may explain the contrasting efficacy observed between pre-clinical and clinical trials of ARV-microbicides. Additionally, CV physiological factors (hormones, immunoregulatory proteins, microbes, pH) and microbicide candidate ARV's (dapivirine and darunavir) were shown to modulate expression of ARV-relevant drug transporters in CV cell lines. This highlights the potential intra-variability and inter-variability challenges associated with microbicide development and optimisation, in addition to potential drug-drug interactions in combination ARV-microbicides. Modulation of cellular pharmacokinetic properties in response to physiological pH levels and pro-inflammatory cytokines, observed within drug transport experiments, further emphasises these challenges. Molecular cloning experiments demonstrated the potential to develop a robust high throughout in vitro screening tool for the development of optimised microbicides. In conclusion, this thesis provides evidence exposing the limitations of pre-clinical CV models commonly used during ARV-microbicide screening, development and optimisation. The potential clinical implications of physiologically-induced and ARV-induced modulation of ARV accumulation in the CV tract when topically applied is highlighted within this thesis. It is imperative these key factors be incorporated into the pre-clinical screening and development of optimised microbicides.