Objectives Partner notification (PN) following sexually transmitted disease (STI) diagnosis is a key strategy for controlling HIV/STI transmission. Anonymous partnerships are an important barrier to PN and often associated with high-risk sexual behaviour. Limited research has examined the profile of men who have sex with men (MSM) and transgender women (TW) who engage in anonymous sex. To better understand anonymous partnership practices in Lima, Peru, we assessed participant-level and partnership-level characteristics associated with anonymous sex among a sample of MSM and TW recently diagnosed with HIV/STI. Methods MSM and TW diagnosed with HIV/STI within the past month completed a cross-sectional survey regarding anticipated PN practices. Participants reported sexual partnership types and characteristics of up to three of their most recent partners. Using a Poisson generalised estimating equation model, we assessed participant-level and partnership-level characteristics associated with anonymous partnerships. Results Among 395 MSM and TW with HIV/STI, 36.0% reported at least one anonymous sexual partner in the past 3months (mean of 8.6 anonymous partners per participant; SD 17.0). Of the 971 partnerships reported, 118 (12.2%) were anonymous and the majority (84.8%) were with male partners, followed by 11.0% with female partners and 4.2% with transgender/travesti partners. Partner-level characteristics associated with increased likelihood of having an anonymous partner included female (adjusted prevalence ratio (aPR) 2.28, 95% CI 1.05 to 4.95, p=0.04) or transgender/travesti (aPR 4.03, 95% CI 1.51 to 10.78, p=0.006) partner gender. Conclusions By assessing both individual-level and dyadic-level factors, these results represent an important step in understanding the complexity of partnership interactions and developing alternative PN strategies for Latin America.