Annual population-based estimates of the number of men who have sex with men (MSM) with diagnosed HIV infection (HIV prevalence pool), and the proportion of all MSM this represents (HIV prevalence), have been insufficiently described over the long term. We investigated the dynamic effects of ongoing HIV diagnoses, lower mortality due to treatment and growth in the MSM population over time on these two epidemic indicators using national HIV/AIDS surveillance data in New Zealand, 1985-2009. The diagnosed HIV prevalence pool rose 79% between 1989 and 1999, and 137% between 1999 and 2009. Estimates of diagnosed HIV prevalence as a proportion of MSM were 0.2% of MSM in 1985, and were between 1.5% and 5.0% of MSM by 2009. New Zealand continues to have a relatively low-prevalence HIV epidemic among MSM; however, the number of MSM living with diagnosed infection is growing rapidly 25 years after HIV testing was introduced.