OBJECTIVES: Numerous HPV models have been developed to evaluate the cost-effectiveness of HPV vaccination.  However, uncertainty remains in some key model parameters such as the risk of transmission and partner formation and dissolution rates.  We attempted to identify those parameters that influenced most calibration fits for an HPV type 6/11 agent-based model. METHODS: We developed an agent-based HPV model of HPV 6/11 infections and disease (warts) to explore the effect of partnership formation and natural history parameters on how well the model output fit observed data on HPV 6/11 infections and disease.  Our heuristic model describes the population in terms of the three groups by individuals’ sexual activity level. The activity level is positively correlated with the risk of infection transmission or acquisition. Persons belonging to the low and medium risk groups tend to have long lasting relationships with low probability of forming concurrent partnerships, whereas those in the highest risk (most active) group tend to engage in short and often concurrent partnerships. RESULTS: We found that the most sexually active group of people is responsible for forming a power-law tail in the partnership statistics reported in surveys and has the biggest impact on the infection spread, and that durations of short-term partnerships, along with risk group and age mixing patterns, have the biggest impact on the model fit. In combination, these factors also determine the characteristic shapes of the warts age-specific incidence curves with the peak occurring in the female population approximately five years earlier than in the male population. CONCLUSIONS: The transmission dynamics of HPV 6/11 infection and disease depend greatly on the short-living partnership networks. Accounting for the formation of such partnerships is critical to achieving acceptable model fits.  Further research is necessary to explore how accounting for partnership formation affects cost-effectiveness analyses of HPV vaccination strategies.