Background: Methamphetamine (MA) use is associated with sexual risk behavior as well as systemic and mucosal inflammation, suggesting parallel biological and behavioral mechanisms of HIV transmission among men who have sex with men (MSM) who use MA. Data evaluating the combined biological effects of MA use with concomitant rectal gonococcal and/or chlamydial (GC/CT) infection on inflammation are limited.Setting: Secondary analysis of stored rectal and plasma specimens from 100 MSM participating in an NIDA-funded longitudinal cohort in Los Angeles, CA.Methods: This cross-sectional analysis evaluated systemic and rectal inflammatory markers under 2 conditions: (1) recent MA use (by urine drug screen) and (2) rectal GC/CT infection. We evaluated 50 participants with recent MA use (25 with and 25 without rectal GC/CT) and 50 MSM without MA use (25 with and 25 without rectal GC/CT). Log-transformed plasma and rectal immune markers were regressed on MA exposure and rectal GC/CT, controlling for HIV status and age.Results: Median age was 32 (range 19-45) years, and 58% of participants were living with HIV. Plasma tumor necrosis factor (TNF)-a, interleukin (IL)-6, IL-8, IL-1ß, and rectal IL-6 were associated with rectal GC/CT and MA use, independent of HIV status. Higher levels of rectal TNF-a, IL-1ß, and IL-17a were associated with rectal GC/CT.Conclusions: Systemic and rectal inflammation was positively associated with rectal GC/CT and MA use. Condomless sex in the setting of GC/CT-and MA-induced immune activation may provide a basis for synergistic biobehavioral mechanisms that promote HIV/ STI transmission among MSM who use MA.