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Phylodynamic analysis and epidemiologic data identified 3 patterns of spread of primary human immunodeficiency virus type 1 infection (PHI) among men who have sex with men (2001–2009): 420 unique PHIs, 102 small clusters (2–4 PHIs per cluster, n = 280), and 46 large clusters (5–31 PHIs per cluster, n = 450). Large clusters disproportionately increased from 25.2% of PHIs in 2005 to 39.1% in 2009 (χ2 = 33.9, P < .001). Scalar expansion of large clusters over 11 months (interquartile range, 3.5–25.5 months) correlated with cluster membership size (r2 = 0.174, F = 4.424, P = .047). PHI cohort data revealed variations in social networks and risk behaviors among the 3 groups, suggesting the need for tailored prevention measures.